I seem to remember being taught in school that the native american reservations exist because of treaties signed by the united states government with sovereign nations (those nations being the native americans) and that the US government is obligated to respect their autonomy and sovereignty by the terms laid out in those treaties.
i don't mean to contradict your claims that the Federal Government has a long history of violating these treaties, as that is undoubtedly true. i'm just curious because the way i interpreted your description makes it seem as if they're only autonomous because the federal government has chosen to recognize them.