The sad fact is that Manhattan is woefully short of marinas allowing passenger pick up and drop off, outside of the large ferry terminals.
The options in the city are North Cove Marina and Pier 25, both in Tribeca, and 79th Street Boat Basin.
There are also places near, but not in, Manhattan- Liberty Landing marina in Jersey City (right next to the Statue), and ONE°15 marina near Brooklyn Bridge (on the Brooklyn side of the river).
We charge an additional $500 flat fee for pick-up and drop off outside of our home base in Sheepshead Bay, Brooklyn. This fee includes getting the boat there and back and all marina surcharges.