The National Archives and Record Administration has the records of the Bureau of Indian Affairs, which operated schools for American Indians. The archival holdings are listed at: http://www.archives.gov/research/native-americans/bia-guide/schools.html. The federal government started making education policy for American Indians as early as 1819 with the Indian Civilization Act, which authorized funds to be granted to religious and private groups to school American Indians. (On the boarding schools, see here.) Eventually, the U.S. government itself via the Department of the Interior’s BIA began operating its own schools.
Federal Education Policy History 