If you've never been to NY Penn before, then 45 minutes is a reasonable suggestion in order to give folks time to navigate their way from street/subway to train platform. Otherwise (and this is basically true across the Amtrak system) the only cutoff is whether you are physically on the train when it pulls out of the station.

The exception is if you are checking bags, in which case Amtrak does have a stated 45-minute cutoff.