We have a couple of books on the third floor that look like good starting points for research.  The first is called Indian Country, God's Country:  Native Americans and the National Parks.  Its call number is E 98 L3 B87 2000.  There's also American Indians and National Parks, which will be nearby on the shelf at E 98 K25 1998.  I found these by doing a very broad search on our home page, just typing in "native american national park."  You will be able to get more specific results by doing seraches using the subject headings for each of those books (Indians of North America - Government Relations, for example), and by using more specific keywords or names, like Yellowstone.