No one really cares or monitors what bags you bring onto the train, so I wouldn’t bother checking in bags or paying the extra bag fee. Just show up 15-20 mins before the train leaves (or 30 mins ahead of time if you’re the anxious kind) and walk on with your stuff when the train is open for boarding. For reference, I do the BOS - NYC - BOS trip on Amtrak every 6-8 weeks and have never seen anyone have an issue with luggage.