I've had zero experience with archival research in the US, but I just recently got done reading Washington's Spies, Alexander Rose's very competent history of the Culper spy ring (which included a small number of female members.) I just did a quick search to see where the archival sources Rose relied on might be found, and came across this magazine article, which says:

Material exists on the Culpers in the East Hampton Library’s Long Island Collection and the New York Public Library’s Emmet Collection, including Robert Townsend’s business ledgers and the Alexander Hamilton-John Laurens letter. The New York State Archives holds the documents found on John André, and the Library of Congress’ George Washington Papers contain most of the correspondence between the Culper members. Other collections hold smaller gems, such as Benjamin Tallmadge’s memoirs at the Fraunces Tavern collections in New York; the Townsend Family Papers at the New-York Historical Society, the Oyster Bay Historical Society, and Raynham Hall in Oyster Bay, Long Island; and Benedict Arnold’s receipts at Laval University in Québec City. Most of the correspondence that negotiated Arnold’s treason is contained in the Sir Henry Clinton Papers at the University of Michigan’s Clement Library.

Hope that helps a little. Good luck with your thesis!