This animation shows wind vectors and modeled water elevations caused by tropical cyclone Irene from Cape May to the eastern end of Long Island, and up the Hudson River. A zoom-in to the New York City area is shown to the right. Sea levels in the animation are controlled by the storm surge blown by the wind, but also by regular tides which you'll note are typically are out of phase (alternate) between the open coast and Long Island Sound.
The research, including comparisons of observed and modeled water elevations, is summarized in a published, peer-reviewed paper:
Orton, P. M., N. Georgas, A. Blumberg, and J. Pullen, 2012. Detailed Modeling of Recent Severe Storm Tides in Estuaries of the New York City Region, J. Geophys. Res., doi:10.1029/2012JC008220, in press.