It is safe to assume that as the population of the United States and New York continue to grow (and there's no reason to believe that trend would not continue as in the past) then there will be more traffic in terms of pleasure boats and trade ships. This pressure tends to have an environmental effect not only from pollution but from habitat encroachment and which kind of aquatic species are still able to live there.
But the larger long term effect will likely come from Climate Change. The temperature of the waters and currents in Long Island Sound are likely to increase, and even a slight difference can have profound impacts on marine habitat. In addition, climate models suggest there will be a rise in sea level over the next 50 years, and possibly a dramatic rise. This changes the shape and nature of the coastline of the sound as well as low-lying areas that will likely have flooding problems, such as...Manhattan Island.