I strongly recommend the Yale Indian Papers Project, http://www.library.yale.edu/yipp/ On the site your students can access digitized (very high quality), transcribed, and annotated documents relating to Native communities and peoples from Yale University, the Connecticut State Library, the Connecticut Historical Society, the Massachusetts Archives, and the UK's National Archives. It is relatively new, and absolutely marvelous.
Welcome to H-AmIndian!
Welcome to H-AmIndian, a joint project between Arizona State University and H-Net Humanities & Social Sciences OnLine. H-AmIndian provides a forum for scholars, academicians, and Native peoples to consider the history, culture, ideas and events relating to Indigenous peoples from the North Pole to Mexico.
The University of Washington Libraries Digital Collections include numerous primary sources:
There's also the NW Digital Archives:
Although it is geared more for middle school and high school teachers, this site includes numerous primary documents, if you want to include Alaska:
The DPLA has an exhibit titled "History of Survivance: Upper Midwest 19th-Century Native American Narratives" (http://dp.la/exhibitions/exhibits/show/history-of-survivance). There are probably more resources throughout the DPLA collections that are relevant as well.
Here is Dickinson College's flickr set of images from the Carlisle Indian School: https://www.flickr.com/photos/dickinsonlibrary/sets/72157605091893725/
In my experience, the "before" and "after" pictures are particularly striking for students.