The MTA will close the doors and go once they feel it's time to do so. They don't care if people are still getting off and on. If you stand on the platform and wait for the lollygaggers to get off the train, they will close the doors and leave.

If you want to get on the train, you can't always wait for the last minute people to get off. Occasionally I've seen people blocking people from getting off, but usually there's still room for them to do so.