That has already happened, shit ain't gonna happen again unless they get guns on the plane. The TSA is worthless, but not that worthless. *note: not saying that a Cessna won't be used, but that's not the scenario that you've devised.
NYC has a radius of at least 5 miles, how are you going to shoot down a plane big enough to "kill thousands" without creating huge amounts of collateral damage? How are you going to determine where a jet is heading from that far out? The Sears Tower might be justifiable as it's right over the lake, and conceivably in the flight-line of O'Hare, but by the time it deviates you won't have something close enough to do anything about it