Your ship will depart from the New York City Passenger Ship Terminal in Manhattan (see link: http://www.nypst.com/
.) Specifically, you'll be leaving from Pier 90, located at 12th Avenue at around West 50th Street.
Islip is located on Long Island, which is about 40-50 miles east of Manhattan. I don't have first-hand knowledge of the hotels in the area. What are your plans to get to the pier in the morning?