I have ridden the subway in the middle of the night (as late as 2:30 AM and as early as 4:30 AM), but not on the A line. But I doubt it's significantly different.

Wait for the train in the middle of the platform, and board the car that has the conductor (or look for the "conductor stops here" sign). The conductor's car always has passengers. Desertion is the problem, not time of day.