Was the trip boked as one journey, i.e. did you just book once, or 2 seperate trips for each leg? If you booked it once under one trip you will need to collect baggage, leave arrivals, then check in again at the main desk.
If you are issued your boarding pass at the Aer Lingus desk for your second flight you pick your bag up in New York, go through security screening for baggage, then pass through connections.
All airports in the US require you to pick up your bag at connections i believe.