Or just something as simple as a rifleman riding in the cargo bay of a helicopter...match speed with a smaller aircraft and shoot the cockpit area up.
Inside of NYPD's airspace, you'll never get the chance to scramble a bird with a marksman in it, intercept, and match vectors within acceptable distance (500 yards? In a vibrating helicopter at a moving target? 300? 100 yards? I've heard the prop-wash actually shoves the bullet down about a foot as it exits the barrel...) to shoot up a cockpit. And you won't break the craft apart, which is the goal of airborne violence over a metro area. Those 737's that hit the Trade Towers were incendiary missiles. If they broke up over Manhattan into half a dozen pieces and rained burning jet fuel over town there would have been bad things that happened, but nothing on the scale of 3000 lives and trillions of dollars of economic impact.
The whole point of interdiction is to prevent the improvised missile attack, using a craft as an explosive delivery device. For that, you have to blow it up or smash it into little bits. Even if you headshot the pilot, the craft is still going to more or less go straight until it crashes into its target (within NYPD air space, you are looking at mere seconds between successful head shot and the bird hitting its target).
Nope. We already know that NYPD and DHS have Predators over NYC.
I'm betting that rather than a SAM system, they have constant airborne assets attached to their Predators.
You're just not shooting down a passenger jet with a rifle. Even a super-evil Barrett.