Heat84 Pipes likely, as well as other things as I said the city is old, it also has a certain fascination with rooftop water tanks which may not be well maintained. A pile of pigeon poop or the occasional dead bird (or even body) could be floating inside one. It starts off in good shape, much like the Internet service, it's the last mile or so that can really screw things up.
May cities draw water from rivers they dump their treated (and untreated sewage back into), others draw from wells that are out drawing the infill rate of the aquifers they use. Even cities that pull from the Great Lakes are having issues with several things including toxic algae blooms. Overall its a bleak picture for most, but for NYC they do have protected headlands which will help them.