Tempest is dead on. I avoid the Gate at slack as it can be full of tugs and barges. I prefer the sleigh ride in either direction. Going north I am usually on my way to Port Jefferson so I prefer a good push. Going south I am usually headed to either Atlantic Highlands or even Barnegat Bay on the Jersey Coast so I like the boost out thru NY Harbor.
We have made the run from Northport to Barnegat a few times.
Bubbles the scenery and sounds of the city are spectacular, We have albums of city shots of the Empire State, Statue of Liberty, Wall Street, South Street Seaport. The UN (disappointing).
The angst about Hell Gate is overblown IMHO. It is to be respected and you dont want to fight current, but the area leading into the East River and to the Manhattan bridges is way more nerve racking.
I used to run the concessions at Ellis Island and never grew tired of looking at the city, and the Lady Liberty. No matter how many times you look at it is still takes your breath away!