There's a shuttle to Newark Airport, check at the Ground Transportation counter when you arrive. Amtrak's Northeast Corridor train from Penn Station stops at Wilmington. To get to Penn Station, you can take a taxi ($45+tolls+tip), NYAS express bus from your terminal ($15) or Airtrain from your terminal to Jamaica Station to the E subway ($7.25) or LIRR ($13) to Penn Station. Taxi or bus might be fastest to Penn Station, LIRR next fastest (I've made it from terminal to Penn Station in 40 minutes).
There's a shuttle to Newark