New York Waterway, the nation’s largest privately held ferry service and cruise operator, does a 90-minute Skyline tour that takes in all the major sights, like the Empire State Building, Statue of Liberty, and Brooklyn Bridge. They also offer a staggering amount of different sightseeing options, including a very good 90-minute Twilight Cruise, Shades of Autumn tour, and baseball cruises to Yankee games.