If he's studying in Stony Brook, then JFK is the better airport to fly into for a direct flight barring any other exigencies.

If he's willing to connect, he could fly into the much-more-convenient airport of ISP (aka Long Island MacArthur Airport), though he would be restricted to flying US Airways through Philadelphia for a through connection.

Assuming he'll be flying in to JFK, if he has a lot of luggage, then a shared-ride service would probably be the best and most cost-effective way to get to Stony Brook. I hadn't ever used such service myself when I lived on Long Island, but you could look into Supershuttle, which operates at many airports across the country, including JFK. If he didn't have so much luggage, we could take the AirTrain to Jamacia station on the LIRR and take a Port Jefferson Branch train to the Stony Brook stop, with a possible change of trains at Huntington.

If he's willing to fly in to ISP, he could simply pick up a cab there or use a shared-ride service. Stony Brook is only around 12 miles from ISP, whereas JFK is about 51 miles away.

This is all assuming the SUNY campus he'll be at is Stony Brook, which is the major SUNY research institution on Long Island.

Feel free to PM me, I used to live in that area and used to travel to ISP/LGA/JFK quite frequently.