Animals have a pretty keen sense of weather, so maybe all the rats who knew a thing or two ran to higher ground. The others...
I find it to be a little ridiculous and naive that people thought that rats would be washed out in waves by the storm surge.
That's like thinking you can out-swim a tsunami.
Swimming is one thing, but no one considers that the wave is moving faster than most people can run (never mind swim!) and is loaded with plenty of sharp debree that will knock you over before you even have a chance to think about swimming.
Also I don't know if the sewers or the subway are really a place a rat would want to be. There would be water and possibly even temperatures, but not that many dry places to nest, low number of food sources (rats also love to eat insects / dog food), frequent water surges... it doesn't seem all that ideal a place for a rat to live to me.
I think if I was a rat I'd want to live only a few yards away from a ripe dumpster, and only a few feet under the ground.