I agree that this is nothing like the Green Line flood in Boston. That was one line, with catenarary rather than a third rail, and not connected by rail to any of the other lines. The city was intact around it, with no other major disaster damage or power outages etc to occupy repair crews.
Is the water mostly in the low parts of hte tunnels under the east river, or are stations flooded, too?
My big question for the New Yorkers on the board is this: What do the city the state and the transit agencies do if they can't restore service in the tunnels for a week or two or more, but the city is ready to go back to work in just a few days? Do they rent all the buses they can and run massive shuttles? Does the city ban driving on arterial streets into Manhattan to allow fast continuous bus replacement service?
I've heard the suggestion of floodgates for the future. I'm inclined to think that they would cost more than repairing the system every fifty or one hundred years, and so should be put off unless we get a substantial rise in sea level from globabl warming, but what do you who know the system better think?