You can take AirTrain on track 1 from your terminal to Jamaica Station, from there you have a few alternatives depending on where in Manhattan you are heading; E subway to midtown (west along 53rd St and then down 8th Ave to lower Manhattan-World Trade Ctr), J subway to lower Manhattan and LIRR to Penn Station (33rd St/7th & 8th Aves).
You can take AirTrain on