Photo Archives, Museum of the Rockies (Montana State University-Bozeman)
From the web site, "The Museum's Photo-Archives collection contains over 80,000 photographs," including some from the Crow Indian Archives of the Little Big Horn College.  For some examples, see the web page of the Elsa Spear Byron Collection.  From the Museum of the Rockies web site.

Online Western History Photography Collection (Denver Public Library, Colorado)
From the web site, "Our on-line collection contains a selection of historic photographs from the collections of the Denver Public Library Western History/Genealogy Department and the Colorado Historical Society."  Try searching the collection for a tribe you are interested in or check the sample subject list for more subjects.  From the Denver Public Library web site.
 
American Historical Images On File: The Native American Experience
From the web site, "This collection of historical photographs is ... a comprehensive collection of images of Native American people. The collection is arranged chronologically from the prehistoric period and the Paleo-Indians to 1990...The collection includes information and images which describe the lifeways of various tribes and include historical entries for particular Indian groups. Narrative is provided that provides the historical and cultural background describing the event, person, or subject presented." From the web site of the American Indian Studies department of California State University, Long Beach.

The web site doesn't have an index or a search engine, so here's a list of the images included on each page.
 
Pre-Contact to 1600
The First Migrations From Siberia
The Eskimo Kayak
The Eskimo Igloo
Eskimo Storehouses
Eskimo Woman Dressed for Winter
The Ancient Mound Builders: The Great Serpent Mound
The Anasazi: Ancient Cliff Dwellers of the Southwest
The Southwest: Prehistoric Pueblos
Walpi Pueblo
Acoma Pueblo
Taos Pueblo
Early Native American Weapons
Bartolome de Las Casas
Documenting the Indians of Florida
Champlain and the Iroquois
The Iroquois Confederacy: Six Nations and the "Great Peace"
Hiawatha
Seasonal Migrations on the New England Coast
An Algonquian Shaman
The Indians of California Greet Sir Francis Drake
The Arrival of the Colonists in Virginia
The Virginia Indians: The Town of Secota
The Virginia Indians: Canoe Building
The Virginia Indians: The Manner of their Fishing
 
1600 to 1750
The Virginia Indians: Powhatan
Pocahontas and the Virginia Settlers
Opechancanough and the Pamunkey War
Corn and the Indians of the Northeast
Massasoit's treaty with the Pilgrams
Samoset Greets the Pilgrims
Roger Williams and the Narragansett Indians
John Eliot: Puritanism and the Indians of New England
King Philip's War
The Pequot War
The Pequot Indians Petition the Colonists
Indians and the Jesuits
Jacques Marquette
William Penn and the Indians of Pennsylvania
The Deerfield Massacre
The Tuscarora War
Bison Hunting Methods Among the Natchez
Native Americans and Moravian Missionaries
Tomochichi
View of Fort Johnson, New York
 
1750 to 1800
Joseph Brant
The Defeat of General Braddock
Hendrick and the Battle of Lake George
The Diplomatic Aftermath of the Cherokee War
Stalking Turkey and the Cherokee Delegation to Britain
Colonel Bouquet: Victory Over the Indians of Ohio
Benjamin Franklin and the Paxton Mob
Samson Occum and Indian Education
Pontiac
Pontiac's Rebellion
The Proclamation of 1763: British Settlements and the Eastern Indians
George Rogers Clark
Scalping and Indian Warfare
Indians During the Revolutionary War: The Murder of Jane McCrea
Land Cessions in Ohio Territory: The Meeting at Fort Harmar
The Washington Covenant Belt
Little Turtle
The Battle of Fallen Timbers
 
1800-1830
President Jefferson and Westward Expansion
The Lewis and Clark Expedition
Sacagawea, Interpreter for Lewis and Clark
Indians and the Fur Trade
Indian Agents and the War Department
Native Americans and European Diseases
Cornplanter
William Augustus Bowles
Tecumseh
The Battle of the Thames
William Henry Harrison and the Battle of Tippecanoe
Tenskwatawa
A Creek House:Influence of the Europeans on the Indians
The Outbreak of the Creek War
Aftermath of the Creek War
Menawa
William McIntosh
Wabaunsee
Jackson at Pensacola: The First Seminole War
Carl Bodmer and the Plains Indians
Plains Warfare: The Kansa War Dance
Burial Rituals of the Kansa
The Dog Society of the Minnetaree
The Bear Dance
Keokuk
The Trail of Tears

1830-1850
Sequoya
The Cherokee Alphabet
Elias Boudinot and the Cherokee Phoenix
John Ross
John Ridge
The Cherokees Arrive in Oklahoma
Allen Wright: Oklahoma and the Choctaw Indians
Choctaw Burials
Black Hawk
The Battle of Bad Axe
A Seminole House
The Second Seminole War
Osceola
Billy Bowlegs
The Second Seminole War: Anti-Indian Sentiment
A Delegate to the Great White Father
Anti-Indian Sentiment on the Frontier: A Massacre Broadside
Thomas L. McKenney
The Chippewas: A Birch Bark Wigwam
Episcopalians and the Chippewas: The Church of St. Columba (Gull Lake, Minnesota)
Red Jacket
The Council of Prairie Du Chien

1850-1875
A Wichita Village
Fort Simpson and the Hudson Bay Company
Haida Buckskin Tunic: Animal Symbols of the Northwest Coast Indians
Shamans of the Northwest Coast: A Tlingit Shaman's Amulet
The Pacific Northwest:Totem Poles
Kwakuitl Women: Customs of Status
A Nootka: A Longhouse
The Plains Forts
Indians and the Wagon Trains of the Frontier
Colonel Stephan Kearny and the Oregon Trail
The Treaty Conference with the Santee Sioux
Henry Rowe Schoolcraft
Thomas Fitzpatrick and the Fort Laramie Treaty of 1851
Isaac Stevens
The Walla Walla Council
General William S. Harney
The Pima: Intertribal Warfare in the Southwest

1864-1874
Bosque Redondo and the Long Walk of the Navajo
Manuelito and the Navajos
The Navajo Family
Navajo Weaving
Origins and Uses of the Peace Pipe
White Settlers and the Santee Uprising
The Union Army Generals and the Western Frontier
The Fetterman Massacre
The Cheyenne Against Custer's Seventh Cavalry
General Hancock: Retaliation Against the Cheyenne
The Medicine Lodge Treaty
Satanta
Washakie
Fort Union Under Attack
The Battle of Beecher's Island
Black Kettle
The Battle of the Washita
Spotted Tail
Father Jean Pierre De Smet
Red Cloud
The Peace Commission and the Fort Laramie Treaty of 1868
Red Cloud Meets President Grant
Ely Parker
Indian Land for Money: Government Annuity Payments (Chippewa in Wisconsin)
Satank
Captain Jack
The Modoc War
Toby Riddle, Interpreter for the Modoc Peace Council
The Murder of General Canby

1875-1890
Custer's Wagon Train Arrives in the Black Hills
The Battle of Rosebud
General Custer and His Indian Scouts
The Battle of Little Bighorn
Crazy Horse
The U.S. Cavalry Adapts to the Plains
Cavalry Troops at Fort Custer, Montana: The Military Responds to Little Bighorn
Ranald MacKenzie
Sioux Prisoners from the Battle of Slim Buttes
General Nelson A. Miles Meets Sitting Bull After the Battle of Little Bighorn
Sitting Bull
The Pictogram: Sitting Bull's Autobiography
Gall
Chief Joseph
Looking Glass
Quanah Parker
Life on the Reservation: Scavenging for Beef
The Peyote Ceremony and the Native American Church
The Bannock War
Carl Schurz and the Department of the Interior
The "Iron Horse" Comes to the Plains
Life on the Great Plains: The Role of Women
The Buffalo Hunt
The Plains: Products of Buffalo
The Carlisle School for Indians
Helen Hunt Jackson
Buffalo Bill Cody
The Native American in Popular Culture: The Cigar Store Indian
Two Guns White Calf and the Buffalo Nickel
Commercial Exploitation of Native Americans
The Indian Police Force on the Reservations
James McLaughlin at Standing Rock
Indians, Indian-related Policies, and the Media
Geronimo and the Apache Wars
Geronimo en Route to Fort Marion with Apache Prisoners
Geronimo Meets with General Crook
Geronimo Surrenders
Life on the Apache Reservation: Measuring Cloth Rations
The Dawes Severalty Act and the Cherokee Strip
Creek Council Meeting: The Final Fate of Indian Territory
Alice Cunningham Fletcher
Crow Prisoners Under Guard
Little Wolf and Dull Knife
Cheyenne Prisoners from Dull Knife's Band, 1878

1890-1900
A Navajo's Trading Post
A Navajo Silversmith
The Pueblo Indians: Baking Bread in a Horno
The U.S. Army and Law Enforcement
A Petition from the Hopi to the U.S. Government
The Hopi Bean Planting Ceremoney
The Southwest: Kachinas
Land Transfers from Native Americans to Whites: 1775-1894 (Map)
Native American Sign Language
Native American Language Families (Map)
The John Powell Surveys, 1871-1879
Sioux Village Outside the Pine Ridge Reservation, 1891
The Aftermath of Wounded Knee
The Casualties at Wounded Knee
The Ghost Dance Movement and Wounded Knee
The Ghost Dance Religion
Wovoka

1900-1950
ADAHOONILIGII, a Navajo Newsletter, Is Published
Charles Eastman
The Society of American Indians
Ishi, the Last of His Tribe
Nostalgia for the Indians in Popular Culture
James Francis Thorpe
Native Americans and Athletic Competition
The Iroquois National Lacrosse Team
The Failure of the Land Allotment System
Indians and the American Legal System
Franklin D. Roosevelt's Policies Towards Native Americans
The Works Progress Administration: Teaching and Education Opportunities for Native Americans
John Collier
The Indian Arts and Crafts Board
The Northwest Coast Indians and Christianity
St Joseph's School at the Menominee Reservation
Ira Hamilton Hayes
Native Americans and Alcohol Abuse
The Progress of Indian Rights Groups
Federal Supervision of Native Americans: The Indian Claims Comission

1950-1990
The Bureau of Indian Affairs Relocation Program
The Iroquois and the U.S./Canadian Border: The Indian Defense League
Industry and Reservations Lands: Protesting a Reservoir
Native Americans and Fishing Rights
Little Big Man is Released
Bury My Heart at Wounded Knee Is Published
Protest Against the Bureau of Indian Affairs
The Trail of Broken Treaties
Clyde Bellecourt
Russell Means
The Siege of Wounded Knee
The Longest March
Louise Erdrich
Wilma P. Mankiller
Mary Crow Dog and Lakota Woman
Leonard Crow Dog
The Revival of Traditional Sacred Ceremonies
The Revival of Traditional Indian Dances
Life on the Plains: The Powwow
Beadwork Among the Seminoles
The Seminoles: Dugout Canoes
Indian Reservations, 1987 (Map)
Native Americans and the Environment
Vine Deloria, Jr.
Native Americans Reclaim Specimens from Museums
W. Richard West, Director of the National Museum of the American Indian