See United States: Presidential Papers for a list of Princeton's microform holdings of papers of US presidents.
For published papers, search the Main Catalog for the president as an author, e.g. Eisenhower, Dwight.
Note that unpublished presidential papers are generally held in presidential libraries rather than by the National Archives. See http://www.archives.gov/presidential_libraries/ for a list with links and addresses.
The American Presidency Project has online copies of major addresses, reports, press conferences, and other documents, including streaming media files, for all administrations.
Public Statements by the Secretaries of Defense, 1947-1981
"Public Statements by the Secretaries of Defense gives researchers their best opportunity to trace the growth and development of the defense establishment in the United States since the Department of Defense was formed in the aftermath of World War II. ... press conferences, background briefings, press statements, and official testimony, along with interview, speeches, and supporting documents, have been collected and organized by the office of the Secretary of Defense." Arranged by presidential administration: Part 1. The Truman Administration (1947-1953); Part 2. The Eisenhower Administration (1953-1961); Part 3. The Kennedy and Johnson Administrations (1961-1969); Part 4. The Nixon and Ford Administrations (1969-1977); Part 5. The Carter Administration (1977-1981). See http://academic.lexisnexis.com/documents/upa_cis/
11230_PublStatementsSecDefPt1.pdf
Documents of the National Security Council (U.S.) History Vault
"Documents of the National Security Council is the only series that collects and publishes all of the formerly classified NSC papers that have been released through Freedom of Information Act requests. The broad range of documents now conveniently available for the first time-including formal policy papers, progress reports, background documents "P" files, "Mill" papers, National Security Council actions, national security action memoranda, and national security study memoranda-gives researchers an unmatched, inside view of the highest level of foreign policy decision making in the Executive Office of the President."
See also the Index to Documents of the National Security Council
Minutes of Meetings of the National Security Council History Vault
See U.S. presidential papers and the regional guides for the important series National Security Files, which documents the foreign policy of the Eisenhower, Kennedy, Johnson and Nixon administrations.