We followed a trip to the Intrepid Museum with the Circle Line Landmark Cruise (1.5 hours), which leaves from Pier 78, just a 10 minute or less walk from the Intrepid. You'll spend a little less than an hour actually underway, as the ferry stops for quite some time in Chelsea. You do get great views of Midtown and down the Lower West Side. Our tour guide was pretty good in pointing out what we were seeing and suggesting things to do in each neighborhood. If it's a hot day, they do have an airconditioned lower section which was nice for our ride back up the river. As with everything, check online ahead of time for discounted tickets. This ferry can get really crowded in the summer as well. While they serve snacks and drinks, you'd do well to come prepared.
Sights:
USS Intrepid Pier, Hoboken Pier, Pier 54 (Titanic Pier), Newport Center, Jacob K. Javits Convention Center, Battery Park, The Museum Of Jewish Heritage, Ellis Island, Wall Street, South Street Seaport and Museum, Brooklyn Bridge, Chrysler Building, Empire State Building, World Financial Center, United Nations