We just did the trip up from Annapolis to Lake Champlain (arrived this past Monday)... through New York Harbor, up the Hudson and through the Champlain Canal to Willsboro. How much you enjoy the Hudson is dependent on the draft of your boat. Currents are wicked on the Hudson down around New York City, but they can also be to your advantage (we did close to 70nm in 7 hours on the way north one day). You also have to fit at least two full days (depending on boat size) to take your mast down and put it back up to traverse the locks (and build braces for it).
The Champlain Canal is beautiful but you need at least two strong people on the boat to get through it. The Hudson River has amazing scenery - West Point, Culinary Institute, Vanderbilt Home, etc. There's nothing like passing under the George Washington Bridge and seeing the little red lighthouse (for the fans of the book) and passing by the Statue of Liberty. The upper harbor was a lot busier for us than the lower harbor (water taxis, tour boats, tugs, etc in the upper harbor). You just have to make sure you stay clear of shipping lanes and channels when you go through the lower harbor. I haven't been through the East River. There are lots of places to visit on both sides of the Long Island Sound.
It's a nice trip (and one I'm incredibly glad we made), but it's a pain since you have to deal with taking your stick down (and the boom off, and all of the associated lines, plus taking off and possibly disassembling your bimini and dodger, etc.) and putting it back up, and not hitting your head on it (or your braces) while it's strapped to the top of your boat. Oh yeah - and making sure the ends don't hit the sides of the locks or that it doesn't get caught at the top of a lock that is going down, and the federal lock in Troy just SUCKS! That just isn't fun. But as much as I complain about the canal, it is incredible.
For guides I used the Champlain/Hudson Cruising Guide (Lake Champlain
) and the canal cruising guide (http://www.nyscanals.gov/exvac/cguide/index.html)
. Navionics charts seem to suck for the Champlain Canal (we were frequently driving on land according to the chartplotter) but were good for the Hudson.
Do you have any other specific questions?