You want to go to Midtown Manhattan and then either take the bus or ferry to NJ. For options in getting to Midtown from the two airports, see:
http://www.flyertalk.com/wiki/index....sportation_FAQ
If your hotel is on River Rd, NJ Transit Bus #158 from the Port Authority Bus Terminal in Manhattan (served by the "E" subway, which is pretty easily accessible from both LGA and JFK) probably stops right outside the hotel. It costs $3.10 per person and runs pretty frequently on weekdays. For the schedule, see
http://www.njtransit.com/pdf/bus/T0158.pdf
You could also take Bus #158 to the Weehawken/Port Imperial ferry terminal and get your hotel shuttle from there if your hotel isn't on River Rd.
If you want to take the ferry, the ferry company runs frequent free buses across town that will take you to the 39th St ferry terminal in Manhattan. You could take any subway and get off at 50th or 42nd for the ferry bus. Or you could take the LIRR to Penn Station and get the ferry bus there if you are coming from JFK.
See
http://www.nywaterway.com/ferry/schedules/ for schedule and route information.
The advantage to taking the NJ Transit bus is simplicity (especially if your hotel is on River Rd), since you would only need three conveyances from the airport to hotel (JFK AirTrain or LGA Q33 bus + E train + NJT 158 bus). The advantage to the ferry is that the ferry ride is fun and scenic, and you don't have to worry about where you should get off the bus.