79th Street Marine Basin
I haven't stayed there (79th street Basin) but I think you can pick up moorings there for $35-$45/night.
I stayed a Liberty Landing a year ago and it was great ! The views can't be beat. The only down side (other than price) was there was no grocery stores within walking distance. You can walk to the ferry for Ellis Island and the Statue. Water taxi to Manhattan from the marina. The marina has a boatyard also.
Don't miss coming down the East River. As stated above, the view is terrific. I have visited NYC many times but Hell Gate to Lower Manhattan on the East River is probably the best way to see the city.