Wirelessly posted (BlackBerry8530/5.0.0.601 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
If by "shuttles" you mean the JFK AirTrain, it should be operating during the hours when you will need it.
If you use the luggage storage at T4, you can take the Q10 or Q10 Limited bus to the A train terminal at Lefferts Boulevard and Liberty Avenue, and not have to pay the $5 AirTrain fare in either direction.