Hi,
There is no easy way on the subway to et to the city from JFK. It really is not a good idea to do it this way. Not sure about buses either, but I'm sure they do run this route.
I would recommend getting a cab from the airport, there is always a 'guard' on the cab line and they organise the taxi queue and make sure you get into a cab safely etc. There is a set fare for the trip from the airport to Manhattan, I think it is around $45, well worth it and you get a good view of the skyline on your way in, far less hassle then having to sort out tickets for buses etc and not being sure where to get off.