1. Watch out for ferries and all commercial traffic. Near the end of a busy day, the southern Hudson river and upper bay can be full of 3' to 5' wakes going in every direction.
2. Those new marinas were made in the shape of boxes, with concrete walls that reflect a lot of wake energy back into and around the marina.
3. Time the currents and tides. Going up the Hudson or East River can give (or take) you over 5 knots of current.
4. Stay out of the way of the ferries