This almost happened in OTL: Category-3 Hurricane Erin was headed towards New York on September 10th, but turned away and headed out to sea.
If it had made landfall, flights out of New York and Boston would've been grounded, thwarting the attacks that day. The hijackers would probably have just gone home and waited another week or two, unless:
A Cat-3 hurricane would have caused even more flooding and power outages than Sandy. If, say, the WTC is blacked-out, the streets around them are six feet underwater, and some idiot accidentally sets their office on fire during the storm trying to use candles, the FDNY might not be able to come put it out, before it spreads to several floors and weakens the girders.