If you are talking about Adventure Cycling's Atlantic Coast route proper, another option is to cycle the bike trail along the Hudson to the Midtown dock for the New York Waterways ferry and take that to Hoboken, NJ, home town of Frank Sinatra and the birthplace of baseball. (Note that if you go on the weekends, the ferry lets you off at the north end of town. During the week, the ferry sails directly to the historic train station. It's an easy ride between the two.) From Hoboken, you can get a train to Port Jervis, NY, which is on the Alantic Coast Route. It's a relatively long (roughly 2.5 hrs.) but beautiful ride. Check New Jersey Transit's web site for schedules and rules about when you can take a bike.
One advantage of starting in Port Jervis is that you get to cycle through the beautiful Delaware Water Gap National Recreation Area, where you might see a bear. From Port Jervis to Lambertville, NJ the route parallels the Delaware River, partially in NJ and partially in PA. It's quite pleasant. If you wish, you can take a shaded, well-surfaced bike path for the last 20 or so miles, from Frenchtown, NJ to Lambertville. And there are two very nice places to camp along this stretch--Worthington State Forest, just across the river from Delaware Water Gap, PA and Bull's Island Recreation Area (reservations recommended on weekends), which is along the bike trail about 8 miles north of Lambertville, NJ.