If you are getting in at 5:45 AM, you shouldn't have ATC delays. But given the ungodly hour, I assume you are on a red-eye from the west coast. You might check the on-time history of this flight. The key variable you have is baggage claim. You will need to go to the lowest level of Terminal A to claim your bags, then go back up to the highest level to get on the AirTrain. From that point, you will be at Terminal B within five minutes, and no more than a further 5 minutes to get to the Virgin check-in.
So I am taking a contrary position. Unless the flight has a dismal on-time history, I think you can make it rather easily. Of course if you have the option of taking a flight that arrives at 5:30 o 5:15, so much the better.