I know MTA has made a lot of flood mitigation investments over the last few years, which should help significantly. In any case, people don't drive or take subways to vote in the big cities -- they walk a couple of blocks. I don't mean to diminish the threat of the storm- it appears likely to result in significant damage. I don't think it's a realistic threat to big-city turnout, however.
I believe it's much more likely to damage turnout numbers in RURAL areas (aka Romney supporters). Driving will be difficult with flooded roads and trees down.
There are more polling places in NYC and Philly than there are in like the entirety of the amorphous blob of red states out west.
edit: This is what I get for quoting a post from like two hours ago.