Re: Hell Gate
I might vote for Inwood Hill Park as your launch site. Only because there's supposed to be parking, there's one subway line, and you can avoid driving through most of Manhattan that way. I'm guessing your trailering the boat, so trailer access (commercial roads) will be needed.
Cannot overemphasize that NYC Parks Dept. is NOT A RELIABLE SOURCE. Make sure to call ahead or email ahead when you first make plans, and then contact them again a month out, and the week before, to confirm they aren't closing the site you plan to use, for any reason.
And you'll want a copy of Eldridge, or anything else that shows the tidal currents around Manhattan, because it is tidal all the way around and your choice of date, route and starting point may be very much affected by this timing. The connection from the Hudson, above Manhattan and down to the Hell Gate, is also called the "Harlem River".
The current timing is all usually based on "High tide at the Battery" or a similar point, so as long as you can find one set of the tidal charts, as you probably know you can offset them from that, you don't need "this year's" book.
There are (or were) some collegiate rowing and sculling clubs on the Harlem River, and there are active canoeing/lkayaking locations on the lower Hudson side, so you won't be alone. There are also a couple of mass water events (swim races) every summer which you want want to miss.
And of course, if you come within a hundred yards of the UN on the East River, the USCG will probably show you no mercy.
Should be one heck of a fun trip though!