PBS
Pbs: The Native Americans
The Corps of Discovery came into contact with "Nearly 50 Native American tribes." This site from PBS discusses the tribes that had the most significant interactions with Lewis and Clark.
Gabriel Dumont Institute
The Metis Men of the Lewis and Clark Expedition (1804 1806) [Pdf]
A five page document in PDF format documenting some of the Metis natives that were involved in the Lewis and Clark Expedition in 1804-1806.
PBS
Pbs: Chinook Indians
Here is an excellent description of the encounter between Lewis and Clark and the Chinook Indians of the Northwest.