Just to elaborate on what ralf said...

Note that if you know you're going to miss the train, you MUST CALL TO CANCEL your sleeper reservation in order to be able to use the funds on another trip, and you actually can use 100% of those funds toward that trip (not 90% and it doesn't matter if your ticket is printed or not; ralf, that 10% surcharge is just for cash/credit refunds issued for tickets already printed—not vouchers for future train travel).

Also keep in mind that the Lake Shore Limited only runs once a day, so you'll have to catch the next day's train if you're headed west of Buffalo (and Amtrak will not put you up for the night on their dime). Also keep in mind that the next day's train's sleeper fare will likely cost more than what you paid, since last-minute fares tend to be more expensive than fares booked ahead of time. And finally, be prepared to find out that the next day's train may even be sold out of sleepers.

My advice? Plan for travel time from JFK to your meeting, and from your meeting to Penn Station and try to make that train.

-Rafi