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"commercial traffic can be pretty heavy and the channel is relatively narrow through HG. " Sometimes, but "narrow channel" means one thing to a hundred feet of fuel barge and another thing for you. They won't be moving very quickly, so you'll all be moving remarkably close to the same speed and that means you can queue up and wait for a break in the traffic in the worst case. Just look over your shoulder on the way down the East River once in a while, and be prepared to step aside.
Less weekend traffic, but honest, I've never noticed traffic in the HG to be a real problem. Often cluttered with oblivious fast-boat drivers racing to make a BBQ on the weekend, they can be worse than the professional mariners.
The high speed ferries...well...a lot of them seem to think they own the water but the bottom line is, they don't. Take due care but don't let them intimidate you. I had the, ah, pleasure of hearing the Staten Island Ferry give a danger horn off the battery one day. I was flaking the sail on a J/24 facing aft when I heard it behind me (ahead of us) and I was not at all happy. Confused too, because I was sure we couldn't be the cause. Sure enough...one of the cat ferry morons had managed to cut off BOTH the USCG Governor's Island ferry AND the SI ferry...I suspect he got more than a polite note in the mail about that one.
If the tides are really inconvenient, note that you CAN overnight in Little Bay, which is just east of the Throgg's Neck Bridge (or Little Neck Bay) and from there just shoot on down to the Hell Gate. Ditto if you pick up a guest mooring at City Island, where the clubs have launch service and there is shoreside food as well.
In good conditions, from the Throgg's Neck to Rariton Bay should be a nice day trip. I'm assuming you have the charts because there is some shoal water in and below NY harbor. The current maps in Eldridge can help make a big difference in the time it takes you to get out past the harbor, too.
And, of course, during the week you've got more freighter traffic coming in the harbor from Ambrose Channel. Treat them like locomotives--they can't stop or turn and they come at you much faster than you think. (Fortunately, like alligators, they can't turn as fast as you can.)