I can't speak to attending the NYC Regional itself, but I have done the New York City subway with a school group (a larger JROTC group back in high school, circa 2003). Some things I'd advise:
1) Make sure everyone has the transit instructions and a working understanding of the system. (That includes making sure they know the trains operate by number or letter, not color...though I think the 1, 2, and 3 trains all stop at both Penn Station and at Times Square where you'd take the S to Grand Central to get to the 7.)
2) Groups, groups, groups. Get everyone into one car if possible, or if you must do two then keep an adult in both.
3) Gather after each transfer on the platform, then move.
4) Strike the fear of (deity) into them if they try to pull a stunt.
