National Security Archive
The website of the National Security Archive includes access to a very large collection of primary sources about the atomic bomb and the end of World War II.
Harry S. Truman Library and Museum
The Truman Library website includes links to lots of primary documents, photographs and oral histories relating to the decision to drop the atomic bomb.
Atomic bomb decision
This website includes links to full-text reproductions of numerous documents from 1945 on the decision to use the atomic bomb. In most cases, the originals of the documents are kept in U.S. National Archives