Harlem River
I am familiar with the Harlem River from growing up nearby, not from sailing it, but there are numerous bridges that would have to be opened for you to make the trip, and my sense is that they almost never are opened. With bridges so close together, you could easily get stuck between bridges waiting interminably, and since there will be no place to tie up and a strong current, it would be an exceedingly uncomfortable trip. I am not even sure there really are tenders on all the bridges, and in addition, several of the bridges have been under construction, so you would need to check with a very updated Notice to Mariners to make sure they are keeping to their schedule. I agree with the others that the route around the Battery is the way to go. But if you should decide to take the harlem River, check this site: http://home2.nyc.gov/html/dot/html/bridges/index.shtml