Many of the Newberry Library's holdings have been digitized and are available via American Indian Histories and Cultures, http://www.aihc.amdigital.co.uk/. This is a subscription service and so may not be readily accessible at many institutions.
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.
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.
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.