Just go through the harbor and under the V-Z bridge. There may be lots of traffic, but the route is shorter and there is plenty of room.once I hit staten island which way is the normal was to go around it? I know it would be busy on the protected side, is it safe to go the open water route? I know weather will be a deciding factor also.
Be certain to monitor Ch 16 and 13. Channel 13 is the channel the big ships talk to each other on. Listening will give you an idea about what they are doing. If there is any question, call them and ask. On the Hudson, you will see barges and small freighters. The channel is narrow in spots, give them plenty of room and when they call you, answer and state your intentions. The hail will be something like: "Southbound vessel, Southbound vessel...."
If you let them sneak up on you, you will find that their horns are very loud!