[7] In addition to providing ferry service, the company also operated three temporary urban beaches in New York City.

The 67.1-foot (20.5 m) Ed Rogowsky, Gene Flatow, Marian S Heiskell, Sam Holmes, and Seymour B. Durst vessels were designed by Incat Crowther of Sydney, Australia and built from 2005 to 2008 by Gladding-Hearn Shipbuilding, and are capable of carrying up to 149 passengers at a speed of 28 knots.

The 53.3-foot (16.2 m) Curt Berger, John Keith, Michael Mann, Mickey Murphy, and Schuyler Meyer Jr. were designed by Nigel Gee of Southampton, England and were built from 2002 to 2003 by Robert E. Derecktor Connecticut Shipyards, LLC, and are capable of carrying up to 74 passengers at 24 knots.

[14][15] New York Water Taxi also operated a shuttle service from Pier 11/Wall Street to the IKEA superstore and Fairway Market, both located in Red Hook, Brooklyn; this service, branded as the "Ikea Express Shuttle", is now operated on weekends only by NY Waterway.

The New York Water Taxi also sells a day pass that travels around Lower Manhattan and Dumbo, which includes admission to the National September 11 Memorial & Museum.