which way through NY?

We are about to begin a tour from Maine to Florida. After looking at both the ACA maps and MapMyRide, we are unsure which route to take through the NYC area. The MMR route goes by ferry from Ct to Long Island, over the 59th St Bridge, across Manhatten to the ferry to NJ. Adventure Cycling swings out to the west. If you have taken either of these route, feedback would be greatly appreciated - BTW we are riding a tandem fully loaded - that means we are longer, slower handling, and wider than most bikes
Thanks