The UC Berkeley site is an excellent introduction to Berkeley's various collections, including the Hearst Museum. A recent addition is AnthroHub which includes full text (or links to) of all UCB serial publications. See also the Native American Studies Collection from the Ethnic Studies Library for many links to full text documents.
"A catalog and online archive of the indigenous languages of California, western North America, and the Americas" - Merged collections of the Berkeley Language Center and the Survey of California and Other Indian Languages, primary strength is indigenous languages of California.
The National Archeological DataBase provides access to the gray literature on archeological sites in the U.S. as well as to NAGPRA texts and information. This database is now included in tDAR, the Digital Archaeological Record.
Kimberly Johnston-Dodds created this website replete with scans of newspaper articles and government reports: it also includes links to her MA thesis and her compilation of Early California Laws and Policies Related to California Indians.
Visit the homepage of the Society for the Study of the Indigenous Languages of the Americas (SSILA) which is a major source for information on Indian languages and language issues. See also: Teaching Indigenous Languages, which includes fulltext documents and many links.
This is the official website of the Hoopa Valley Tribe. It is an extremely rich site - keep looking to find text of many of the primary documents regarding the history of the tribe as well as current Trinitiy and Klamath water issues.
Their mission is "to bring together the language people, advocates, programs, and governments of the local tribes in order to form an alliance that will support language restoration and revitalization efforts."
SODA includes fulltext of many U.S., state, and local documents in three collections: Southern Oregon History; Bioregion (i.e., Klamath-Siskiyou); and First Nations/Tribal Collection (including Karuk, Hupa, Yurok, Tolowa, Wiyot).