While not a strictly CIA operation "Blind Man's Bluff" was a good read on submarine operations during the Cold War, specifically Operation Ivy Bells which detailed the tapping of undersea cables between Petropavlovsk and Vladivostok.

As a former spook, this book still feels wrong to read because of what's in it.

I've never read it, but I've had "Overthrow" by Stephen Kinzer on my to-read list for a while now. Supposed to be about American support for regime change all over the world. I loved his book on the Iranian revolution -- All the King's Men -- so I really should get around to reading this one.