It IS pretty awesome having that B-747 entry tucked in with all those C-172 entries. Having flown over the Big Apple and Washington DC as a passenger at FL360 on many occassions, I can tell you that the WTC, the Empire State Building and the Pentagon are quite identifiable on a clear day such as 9/11 was. I don't think it would be impossible to do it although your theory that the pilots were forced to at least bring the planes to altitude makes sense. When I flew the 747 sim, I did two TO's and landings at LAX, once around at SFO and then again at KaiTak Hong Kong. It was all night flying and for the run into KaiTak and just to make my last landing more interesting, the Chief Pilot turned off the navaids and cleared me for a VFR approach. If you ever had the pleasure of landing at KaiTak you know it is, shall we say, a unique approach. Even then I was able to locate the airport at night without navaids. So, with some training, I do believe the hijackers _could_ have done it themselves.
Approach to KaiTak: Fly base and ignore the admonitions from the radar altimeter to Pull Up as you cross over Stonecutter's Island, then make a
90 degree right turn and dirty up the plane real quick with flaps and gear to get down to the runway. Don't forget to smile and wave at the people in their apartments as you fly by at eye level along the curved approach to the runway.