There's Marine Corps Air Facility Quantico (home of Marine One). Don't know if the strip there is long enough for the planes they show them flying or not, and it's predominantly a heli base I think.
Of course, I'm not overly convinced that the FBI has a crack team of profilers that flies out via private jet to everything like on the show
. My guess is if they have teams that do this that they're far more likely to fly commercial, there's very little that is on the show that commercial schedules would really be a problem for.