Academic Search Premier (EBSCO) is a solid starting place for most research topics. The database indexes thousands of scholarly journals. To limit your search to academic journals, click the Scholarly (Peer Reviewed) Box before you enter your search terms.
America: History & Life is the major database on American history from pre-history to the present. Use it to find articles related to the Native American experience in the United States pre-and post-contact.
JSTOR is a journal archive with thousands of full-text articles. However, because of its archival nature, there will generally be a three to five year window in the currency of the articles. Be sure to explore titles under the Discipline(s) and/or Title(s) American Indian Studies, Anthropology, and/or Archaeology to limit the scope of your search.