How did the 9/11 hijackers find their way to New York City?
Several of the hijackers, including Mohamed Atta, held at least private pilot certificates and had undergone ATP level jet training in DC9 and 737 full motion simulators in December of 2000. Atta himself held a commercial license with instrument and multi engine ratings. They were well versed in aerial navigation techniques and more than capable of navigating the aircraft in question back to New York City and Washington DC after it was hijacked and secured.

A basic scenario that any private or commercial pilot could have done:  the hijackers knew the flights they were booked on and the rough routes they would take to their destinations. A little basic planning amongst themselves would have produced the approximate position the aircraft would be at at the time it was hijacked. 

Once seized and the flight crew liquidated, they could quickly determine their positions either from their headings and next waypoints or with a simple VOR fix (any competent private pilot can do this). The autopilots could quickly be disengaged and the airplanes hand flown using basic pilotage (good weather prevailed over the east coast that morning) or radio navaids to return to their targets. The navigation and flying they did that day was relatively simple.

As an update, I know these kinds of questions float around with “9/11 truthers” and other conspiracy fanatics as some sort of proof that the official explanation is incorrect. Quite often they cherry pick quotes and ignore any other evidence that won’t fit their narrative. Combine that with the public that’s largely ignorant about aviation, it allows these kinds of ideas to fester very well without challenge.