If you're traveling to Brooklyn, JFK is your best option. It's connected by the AirTrain, an airport shuttle that will take you to either the Howard Beach or Jamaica Subway stations. From Howard Beach, you can ride the A line to downtown Brooklyn. At Jamaica, you can opt between the J and Z lines—both of which run through Bushwick and Williamsburg—and the Long Island Railroad, which will have you in downtown Brooklyn in 18 minutes.