A quick search of our catalog search led one of our archivists to this item: Indictment of William Bradford and John Mitchellfrom the U.S. Circuit Court for the Eastern District of Pennsylvania. (These were two who were indicted for stirring up the rebellion as Raising Revenue tells me.) My guess would be to contact NARA Philadelphia, which holds the Circuit Court records for Pennsylvania.
Another archivist suggested searching Founders.archives.gov, which mostly finds official notices about the Whiskey Rebellion, but also a citation to William Hogeland, The Whiskey Rebellion: George Washington, Alexander Hamilton, and the Frontier Rebels Who Challenged America’s Newfound Sovereignty, N.Y., 2006. There are also some detailed reports about the issue that are from RG 58, Letters of Commissioner of Revenue, 1792–1793. For example, this one giving a summary of attitudes in the states: To Alexander Hamilton from Tench Coxe, 19 October 1792. The footnotes for that letter contain lots of links to other letters from the Hamilton Papers.
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Please send your request to email@example.com and an archivist will get back to you within 10 business days. We hold a number of files in RG 21 relating to prosecution of the rebels. The files are not 100% complete, but should be of interest.
The National Archives at Philadelphia