www.archives.gov
There are some good research ideas for researching Indian Census Rolls at https://www.archives.gov/research/native-americans/census/research-indian-census.html
One particularly helpful suggestion was for records prior to 1885, to "consider researching the Congressional Serial Set to find an individual's by name or information about a tribe. The Serial Set contains records received by Congress, primarily from agencies of the Executive Branch, and reports published by Congressional committees. Documents relating to American Indians often address claims against the government for depredations or treaty rights; some include lists of Indians, but they seldom provide any detailed information about the individuals. "
I was excited to learn that these records have been digitized and indexed and are available online at Heritagequest.com.