You can take the Air Train to Jaimaca Train Station, then come down from Air Train Platform to the LIRR (LONG ISLAND RAIL ROAD) tracks take a West Bound Train to New York City Penn Station. (You can pay on train for extra fee or buy ticket before boarding train).
Exit Penn Station on the 7th Avenue side, depending on where you exit you will be either right outside Madision Square Garden on 7th between 31st and 32nd Street, walk left 2 blocks cross 7th and walk 1 1/2 blocks down to Metro Hotel. Or you might exit on 34th Street walk right toward 7th Ave and follow above.
Safe Travels!
Air Train to LIRR