I lean towards, if the CIA themselves didn't directly orchestrate it, a ragtag group of disillusioned paramilitaries associated with anti-Castro activities in Cuba did. There's so much motivation for such groups to partake in the assassination of President Kennedy. You have the failure of the Bay of Pigs, the Kennedy administration pulling the plug on JM/WAVE "Executive Action" schemes, President Kennedy meeting with Khruschev and making concessions in order to resolve the Cuban missile crisis. I set my sites on such groups as those paramilitary agents at JM/WAVE in Miami, Operation 40, Interpen, Alpha 66...some combination of the forces, reactivated and repurposed by some "invisible hand" to assassinate JFK, and keep the fight against Communism going strong.