This ideas is simply not practical and quite farfetched. Firstly, people have been flying from airports from decades, they are not going to simply begin to go to Long Island Sound when they want to catch flight. When people want to catch a flight, they go to an airport because most planes depart from airports, and this is not going to change anytime soon. Secondly, high costs in developing seaplane ports and using seaplanes would deter any airline from entering a seaplane business. Thirdly is the prices for consumers, the prices for seaplane travel are currently high, and will continue to be high because of the costs of running a seaplane service.
Using another airport is much more practical. Currently Newburgh airport is the favorite because of its highway access, convenience for many New Jersey flyers, and proximity to the Metro-North Hudson Line. However, it is about an hour north of New York City. White Plains Airport is convenient to many New York flyers, in New York City and the northern suburbs. West Islip could work well once Long Island Railroad- Grand Central rail link is up and running. West Islip also has ferry service to Bridgeport, CT
and New London, CT