Alright, now for somewhat of a more direct answer: Apparently much if not most of the CIA's flying is now done by contractors. Most of these operations don't exactly advertise, y'know... a bit of time spent with google and a few visits to some 'black helicopter' websites will get you the names of some of the CIA's contractors.
FWIW, a bit of reading might be in order first. I recommend Christopher Robbins' "Air America" as a good start. It deals a lot with the CIA's flight operations in Vietnam and in the closing pages it addresses some of the changes in government (open records, unwanted press, etc) that affected how the Agency operated aircraft.