I was wondering about this last night. Grim:

The 8-million-strong human population of New York City is matched, if not exceeded, by the city’s number of rodent dwellers. Fortunately, the two populations don’t mingle all that often.
But that could change as storm waters from Hurricane Sandy flood rats out of their underground residences, according to Rick Ostfeld of the Cary Institute of Ecosystem Studies in Milbrook, N.Y.
“Rats are incredibly good swimmers,” said Ostfeld. “And they can climb.”
In other words, Sandy is unlikely to knock off the resilient rodents, but rather displace them.
According to Ostfeld, this could result in increased risk of infectious diseases carried by urban rats, including leptospirosis, hantavirus, typhus, salmonella, and even the plague.
“One of things we know can exacerbate disease is massive dispersal,” he added. “Rats are highly social individuals and live in a fairly stable social structure. If this storm disturbs that, rats could start infesting areas they never did before.”
And it’s not only the bite of a rat than can transmit disease. Rodent feces and urine can spread hantavirus, for example. Still, Ostfeld suggested that the huge volume of water Sandy is expected to bring should dilute the pathogens and lessen risks to public health.