Even po-dunk VFDs have more than one 'channel'. NYC should have a wad of them, and emergency communications coordination.
It didn't because the emergency center was in a building in the same complex as the targeted towers.
Still, I would expect one or more mobile commo vans (command centers) which could have handled a localized crisis in a city that size.
It really should have been evident that it was only a question of 'when', not 'if' there would be a problem with that many people in such a small area in a city which is, by virtue of its size (if nothing else), a high profile target.
And although it is not possible for anyone to anticipate every possibility, the WTC had already been the target of one bombing.