As a regular commuter to/from and around Manhattan, what scares the crap out of me are the train tunnels under the Hudson. Amtrak would be the main target (for its name recognition and strong federal government tie), but the New Jersey Transit trains use the same tunnels. After 9/11. they started being very careful about not letting trains get backed up in the tunnels — they’d hold trains outside the tunnel until the one in the tunnel was all the way through or very nearly so. In the past couple of years I’ve noticed they’re not being so careful about that anymore, and it really worries me. These are electric trains, and if somebody takes out the electrical system with 3-4 trains in the tunnel in each direction, that’s a huge number of people in the tunnel, captive for virtually any sort of secondary attack. The terrorists don’t want to do something that looks makes them look weaker than the 9/11 attack, and the train tunnel situation is providing the opportunity for a comparable if not higher body count.
That sounds like a nightmare situation. I hope you have good intuition and listen to it. I use DC Metro sometimes, and there are Metro police all over the place. It makes me feel marginally better, at least I won’t get mugged.