Two things I have learned about JFK Airport:
1) If you have enough time to leave JFK Airport during a transit, you should. They don’t have enough seats for all the passengers here and the air conditioner is weak. On top of that there are flies buzzing around everywhere. It is an unpleasant experience. (Terminal 4)
2) If you are heading into Manhattan from JFK airport I would suggest you take either public transportation (subway) or a taxi. By no means take the Super Shuttle. It is a terrible option. It costs $20 and is a shared-ride van. You have to wait for the driver at the terminal, you then have to wait for your fellow passengers, then you drive to each terminal to pick up passengers, and then it’s up to the driver who gets dropped off first. If you’re the last person dropped off, it may take you 3 hours to get to your destination. A taxi costs $45 (plus tip) and you can leave right away and be dropped off at your exact destination. Subway costs around $7.50 and takes an hour.
You have been warned.