Navigated through NY Harbor many, many times. I'd say 60% of the time it can get pretty rough but then there are times when the water can be like glass, it's pretty amazing. The roughest area is usually where the Hudson comes into the Harbor. Traveling up the east river you should really time the tides and currents. You can get an additional 6 knots in some sections of the east river if you time it right. It's a lot of fun and Hell gate is pretty cool. Wind, current, and ferries are usually the reason it gets so rough but our R25 handles it no problem. Nighttime is even more beautiful with the lights of the city. There is a cool little anchorage behind the Statue of Liberty. There is a marked channel along the southern side that leads back to an anchorage. There is a ramp there and you can tie up for a bit and go to the diner across the street. The anchorage is really nice and holds well and the nighttime views are amazing.
Oh, and traveling under the Verrazano Bridge can also get a bit rough but once you cross over into the harbor it gets much calmer. Have see 3-4 feet at the bridge and 1-2 in the harbor before.