Nobody Could Have Predicted It

Well, actually:

Last fall, as part of a massive report on climate change in New York, a research team led by Klaus Jacob of Columbia University drafted a case study that estimated the effects of a 100-year storm on the city's transportation infrastructure. Considering MTA Chairman Joseph Lhota’s comments today that Hurricane Sandy's impact on the subway was "worse than the worst case scenario," it seems pretty safe to put Sandy in the 100-year category. In that case, assuming the rest of the report holds true, the subway system could be looking at a recovery time of several weeks, with residual effects lasting for months and years.
The researchers modeled a potential 100-year storm that consisted of either a category 1 or 2 hurricane hitting nearby, or a severe nor’easter that coincided with high tide. (As we know now, Sandy was a hybrid of all three events.) The models predicted complete flooding of several tunnels after such an event, including all the tunnels in the East River:

Based on their models, Jacob and colleagues wrote that a 100-year storm could leave roughly 1 billion gallons of water to be pumped from the city’s network of subway tunnels. (To give you an idea of scale, that’s equal to the average daily consumption of drinking water in the city.) If all 14 tunnels flooded, it would take about five days to pump each one clear, according to the report. However that’s the best-case scenario; a week per tunnel is more likely.
Immediate flood-clearing isn’t the only concern. As Ted Mann writes for the Wall Street Journal, salt water is likely to have considerable residual effects on the aging subway system. Jacob and colleagues write that equipment damaged by brackish water will at least require time to clean and could also require time for replacement.

Good job, guys.  You called that one.  We need more of this, and less whistling past the graveyard.  I'm looking at you, GOP.  Science and common sense are our friends, not our enemies.