If your brother does really need to land at JFK, the cheapest reasonable way to get to PHL is by Greyhound bus from Port Authority (www.greyhound.com). Amtrak is slightly more expensive, but still comfortable. Check the Amtrak board on the FT Miles forums for discount codes to use--with the discount, he should be able to make this trip for about $40. If you are looking for super cheap, there is a commuter rail option from Penn Station, taking NJ Transit to Trenton and then SEPTA from there to Philly. But it takes years and involves a train change.

All of these options also involve getting from JFK to midtown Manhattan, which is a time-consuming and money-consuming journey in itself. (Probably the cheapest reasonable way to do that is to take a van or bus shuttle--sorry, I don't know details on these.) If there is any way for your brother to fly directly into PHL, he would save not only money, but many hours of travel time.