Are you paying cash or using points?

Have you considered the Quality Inn in Jamaica?
http://www.qualityinn.com/hotel-jamaica-new_york-NY326
The pictures on the website look very tired, but according to a recent TripAdvisor review the hotel has just been renovated. It is two blocks from the Jamaica station of the LIRR and AirTrain, which could work well for your plan of exploring the city.
http://www.tripadvisor.com/ShowUserR..._New_York.html
It's also only 8K-10K points, so a good value from that perspective (you might consider booking two nights to accommodate your evening departure).

Between the Comfort Inn Jamaica and the Comfort Inn & Suites Ozone Park, I would pick the Ozone Park location due to its newness.