What is the best way to get from JFK to Montauk?
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Take the the AirTrain to Jamaica. At the Jamaica station you can get a Long Island Rail Road train to Montauk.
Check the Long Island Rail Road timetables. There are only a few trains to Montauk and if there's going to be a long wait I think you're better off spending most of that wait at the airport rather than at the Jamaica Station.
Here's the summer timetable, effective May 15th:
It really depends on when you're arriving. The train is fine but doesn't run very regularly. Your other option is the
which runs much more frequently. You'd take a taxi from the airport to the "Queens airport connection" stop of the Jitney off the Long Island Expressway. Their description is:
Our Queens airport connection stop is located at exit 25 Eastbound off the L.I.E. at the corner of 190th Street & the Eastbound Service Road, in front of the Fresh Meadows Cineplex.
You need to book this in advance though.