Answer:
If you don't want to take a taxi, you can take the subway, which costs only $2.25 to date (October 9, 2009), plus the $5 you will need for the shuttle. The shuttle (called the AirTrain) takes you from inside the JFK terminals to the Howard Beach Station of the A train (of the A-C-E, the blue line). You can take the A train straight into Manhattan.