S East Meadow to South Ferry. No idea where exactly you are starting and not sure about the NJ ferry.
This is a lot of bike path or on street lane, and it's fairly scenic. As alternative, you can skip along the Verrazano and take the Bedford Ave. bike lane to Ave. I or so, then over to Ocean Ave. and up and thru Prospect Park. Others can then give advise as to how to get on the Brooklyn Bridge.
http://ridewithgps.com/routes/3616970