I'm actually reading the book Brothers by David Talbot right now. It covers the relationship between John and Bobby Kennedy and includes a pretty good section about how in the 50s the Dulles brothers basically dictated foreign policy. There was a lot of friction when JFK came into office because, especially after the Bay of Pigs, he didn't let them get away with things.

The book does veer somewhat into unfounded conspiracy territory, but I think it's an interesting read so far and the author doesn't come across as crazy so much as skeptical.