Government archives hold permanent records created in the course of business for federal government agencies. Often what you will look for here are published works, reports, and policies; records of government officials; records of specific programs, people, or places; or topical exhibits.
Museums may hold objects from indigenous populations, but often those objects were acquired through colonization and may be represented from a white, European perspective. Always evaluate sources for bias. Seek out organizations that collaborate directly with the indigenous communities that they represent.
Below are some examples:
List of Heritage and Cultural Organizations from Native America Today
Wikipedia page for "First Nations Museums in Canada"
Websites of advocacy groups can be sources of information on policies and practices, current issues, historical background, and places to find additional resources.
Tacking on the word archives to a search of your subject will probably lead you to options for finding websites and holdings of archives. Here are some options to get started!