This is a no-brainer. Arriving into Penn Station via Amtrak, you should immediately buy a ticket on the next departing LIRR Train, since they all stop at Jamaica. Its 1 to 3 stops (depending on local or express) and is quicker and more convenient than the subway.
Just make sure you go ahead and get your tickets for the LIRR in advance because its more expensive to buy on board. Also, theres a good chance they may not even get to punch your ticket by the time you get to Jamaica, which means if you hold onto it, it will be good for the return!