Stephen Ambrose wrote "Undaunted Courage" for a modern take on the expedition.

Donald Jackson compiled contemporary accounts and letters in his 1978 "Letters of the L:ewis and Clark Expedition, with Related Documents"

I suggest you start with the Govt. Archival website:
http://www.archives.gov/education/lessons/lewis-clark/
The University of Nebraska has the text of Lewis and Clark Journals.

The National Geographic site is a good article about the expedition: http://www.nationalgeographic.com/lewisandclark/