U2's and A12's (SR71 predecessor) were flown by the CIA. SR71 flew for the Air Force beginning in 1964 (I think). Finally retired in 1990's. Francis Gary Powers was indeed flying on behalf of the CIA.
If you ever buy a book on aviation, make it Sled Driver by Brian Shul.
I would bet that F4's, 15's or 16's have amassed more time M1 plus than anything else??