I'm in Manhattan, but if you can get an early enough train and are on a line without weekend bike restrictions I would take the LIRR. You will need an MTA bike permit which is $5 for a lifetime permit http://www.mta.info/lirr/about/Bicycles/. From Penn station take an A train or 1 train to 168th St, take the elevator up to the street and then ride to the start. If you want to ride to the start its probably around 8 miles. When you return on the ferry you'll be less than a mile from Penn station. The Gran Fondo just put out their riders guide, you can download it from their website. In it they say the cutoff time for entering the start area on the bridge is 6:15 AM, which means you'll be standing in the cold on the bridge for at least 45 minutes before- arghh. Subway service at that hour of the morning on a weekend is not too frequent either.