I don't know exactly what NYC does for the subway, but I would assume that water in the tunnels (like from a brief downpour or a broken main) could be pumped into the storm drain system and flow out to someplace like the East River or the Hudson. Of course, if the cause of the flooding is because the rivers themselves are running so high that they're flowing back into the subway stations from the street--well, that's a huge disaster and there's nowhere to pump the water to in that case. Then we're getting into doomsday scenarios like kc2ixe was mentioning.