I would redesign it with a 4 Terminal Layout .... Similar to the Current O'Hare Layout..... interconnected and close to each other.
Terminal 1: Delta Air Lines and International Star Alliance Members (Former Eastern and Pan Am Terminal)
Terminal 2: jetBlue Terminal.... Literally an exclusive Jetblue Terminal with Aer Lingus, Hawaiian Airlines and Caribbean Airlines! (Former TWA Terminal)
Terminal 3: American Airlines' and Oneworld Members Terminal. Also US Airways, Spirit and El Al would operate here.
Terminal 4: Mostly a Sky Team Terminal with United, Air China, etc. (Former National Terminal)
I would have Terminal 2 and 3 be in the same building... since AA/Oneworld seem to get along with Jetblue alot, meaning more code shares and possibly reduced fares.
Terminal 1 and 2 would be the most breathtaking because of Pan American World Airways and Trans World Airlines rich history into them.
A huge problem with JFK today is that there is very little on sight hotels or hotel shuttles and you have to take that damn tram to... i think it is Hudson Beach? Correct me if wrong. So I would have both a Sheraton Hotel in front of the terminals (Like The Hilton is in Chicago O'Hare) ... with a Holiday Inn Express right next to it.
The capacity at my JFK could easily be 80-90 million passengers!