The closest subway stop is the Howard Beach Station on the A train (of the A-C-E, the blue line). You can take the shuttle, called the AirTrain, from inside the JFK terminals to the Howard Beach Station.
You can also take the AirTrain to the Sutphin Boulevard-Archer Avenue Station on the E train and the J-Z (the brown line). But the AirTrain ride from JFK to the Sutphin Boulevard-Archer Avenue Station is almost 4 times as long as the ride from JFK to the Howard Beach Station.
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