Having played with mud and water as a kid, I think I have a simple answer:
Construct an emergency sewer system than is deeper underground than the subways, whose flooding with copper corroding salt water would destroy in a very short time period. When underground NYC is flooded, the damage increases exponentially with how long the salt water remains (fresh water is not nearly as serious a problem).
The key to NYC's (Manhattan) survival is not damaging too seriously the buried power cables, fiber optics cables, fresh water lines, brown water lines, subways, steel rail commuter and passenger train lines, etc.
The keys are drainage grade, and, pumps.
EDIT: regardless of the creation of marsh environments, etc., the key will remain the absolute heigth of sea level. The issue, IMO, will not be slowing the water down as much as not letting it in.
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