Peeking into the rock

I'm in the midst of biying my tickets to Prague. One possibility includes a 12 hour layover at JFK, from 8 in the monring to 8 at night. This looks attractive to me, depending on transportation into and out of the city. (I'm going to ask at Making Light too). Has anyone here ever taken the bus (or subway, or whatever) from JFK into New York? How long is the ride really? (I have an informational website here but I feel that direct experience might help understand this). I see there are several routes to different parts of the city. Depending on whether someone wants to meet me for lunch that day, what I envision is probably hitting a museum or two and getting lunch and then heading back to the airport to arrive there around 5:30-6:00 since the next leg of the trip is international.

Any advice? Anybody want to meet me somewhere for lunch? Do you have a better idea?