I agree with Cam about going the southern route around Long Island. Unless you want to sight see dead bodies in the East River.
It can be really crowded there with the commercial boats and very nerve racking, but very do able. We made the trip around the tip of LI to the southern shore and further many times in the late summer. As long as you get around by late september, you should be fine. It is a nice stretch of water if you avoid the storms.