You can cross NYC by using the the bridge that is in the 170's. I cant remember what it is called though, sorry. As for riding through, I rode Boston Post Road a good deal through. I stopped one night in Meriden, CT, the next in Coventry, RI, and the last day was a 50 mile ride to Boston.
Coming back I rode to Tolland, CT, Stramford, the next night, and New York the third. Even though it is out of the way, I preferred the Rhode Island route. Entering CT from MA I was forced to get onto an interstate for nearly 3 miles. Thankfully I was able to exit without incident of any kind.