The easiest way is to take the AirTrain to Howard Beach, and then board a Manhattan-bound "A" subway to Columbus Circle station.
The alternative -- which will probably be a few minutes faster but will involve an additional transfer -- is to take the AirTrain to Jamaica, and then board a Manhattan-bound "E" subway. At Seventh Avenue/53rd Street station, transfer from the "E" to an uptown "B" or "D" subway (on the lower level of the station) for the one-stop ride to Columbus Circle.
AirTrain and "A" subway should take a little over one hour; AirTrain and "E" subway, with a transfer to the "B" or "D" at Seventh Avenue station, should take just under an hour.
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