The Philly Bike Club does a yearly ride from Philly to New York, which I went on last year. The route starts in Philly at the Art Museum, over to New Hope where it crosses the Delaware into NJ. From there, it's mostly calm back roads through NJ until the approach to Hoboken. There, it goes through an industrial area. On the weekend it's very quite and manageable by bike, but I'm told that during the weekday it would be rough. From Hoboken, we take a ferry to Manhattan (bikes are allowed for a nominal charge).
A more detailed description of the ride/route is available here: http://phillybikeclub.org/newbcp/events/nycride2011/nycridemain.html
And the cue sheet: http://phillybikeclub.org/newbcp/doc/rides/NH-NY_Cue_125_08-30-09.pdf