From the New York Times' Dot Earth blog:
MIT
A simulation of the storm surge from Hurricane Irene (using the Slosh model) shows severe flooding in New Haven and New London, Conn., (the scale is in feet) and parts of New Jersey, with extra sea height of around four feet (on top of the tide) in New York City.
Researchers at the Massachusetts Institute of Technology focused on coastal impacts from hurricanes have run fresh simulations of the possible storm surge as Hurricane Irene hits the New York metropolitan region. Simulations using two surge models (known by their acronyms, SLOSH and ADCIRC) found 1.22 and 1.05 meters of surge (4 and 3.44 feet) of surge at the Battery, at the southern tip of Manhattan.
This would pose serious risks to low installations and the subways but is nowhere near a worst case (think 13 feet, as in 1821)....MORE