Protecting the city from a storm surge is a little small-minded. NY worst disasters have been from blizzards (1888), terrorists (2001) and hurricanes ('85, '11, '12). There is no single defense to save the city from all three. Additionally, other cities have been hit by disasters, defending each one against whatever nature can throw would be impossible.
On a national level, creating a disaster 'first-aid' organization which can respond to any event is probably the most effective way to go. (FEMA isn't operating at the level, most of there work is long term recovery.)