Normally if your air draft exceeds 32' you must transit west of Roosevelt Island. The lift bridge on on the east channel will not open if the west channel is open.
The west channel may be closed based upon security threats to the UN. These closures may or may not be in the Notice to Mariners. Recently the port officer has been announcing scheduled closings of the west channel on VHF 16. Further,when the west channel is closed security forces are highly visible at both the north and south ends of Roosevelt Island. They will hail you on Ch. 16. and direct you into the east channel. Failure to respond ensures an imminent visit from armed patrol boats.
If you are directed to the east channel you will need to hail the lift bridge operator. The operator listens to 13, as I recall. The bridge opens on demand but there is a thirthy minute wait as they go through their signal sequence so hail for the opening as soon as you pass the northern end of Roosevelt Island.
There may be whirpools and standing waves -- particularly near Randalls Island. They will be similar those at Plum Gut or The Race. Keep your head up as you round the Battery for brisk ferry traffic. Otherwise the commercial traffic has in my esperince always been very courteous and their behavior highly predictible.
It's a beautiful trip. I always enjoy it.