If you don't want to take a taxi, you can take the subway.
At JFK, you can get a shuttle (called the AirTrain) from inside the JFK terminals to the Howard Beach Station of the A train (on the A-C-E, JetBlack which is the blue line). The A train goes straight through Manhattan.
The subway costs $2.25 and the shuttle costs $5 (as of today, October 16, 2009).
