Seriously, I've transited NY harbor twice. Fabulous experience, surprisingly easy once you do a little preplanning (I overplanned/studied for the first transit expecting it to be like that old "Frogger" game of a frog crossing a highway, with me as the frog).
Work the tides for Hells gate and its a blast. Stay tucked in on the appropriate side and give way to pretty much everything. As per the previous post take an experienced crew with you if you can. Unless you are an absolutely beginner at the boating game its a trip not to be missed.