There really is an "el" (elevated train) right outside the restaurant, and since it has tracks going in both directions, its quite possible to have the sound of roaring trains overhead in quick succession. The downside to the "reality" argument is that the location of the restaurant (White Plains Road & Gun Hill Road) is at a subway stop at which all trains stop, thus the trains wouldn't actually be roaring overhead.

That aside, I always likened the sound of the trains roaring as being symbolic of Michael's life being similar to a runaway train at that point....it was careening out of control, taking him on a (noisy) path of fulfilling his destiny.