Typically, Remicade kicks in much more quickly than 6MP so it's likely that if he started that, he'd be on Prednisone for less time.
They have found that the cancer risks with biologics were really overblown - they are lower than initially thought. I have to say that of the two classes of medications, biologics scare me less and my girls have tolerated them better. Thiopurines like 6MP and Imuran (my daughter is on Imuran) definitely scare me the most and have an additional skin cancer risk.
Both my girls have juvenile arthritis. The younger one also has IBD. She was diagnosed with IBD after being diagnosed with juvenile arthritis and was already on a biologic that treated the arthritis when she was diagnosed with IBD. So the decision to switch to a biologic that treated both the arthritis and the IBD was fairly easy (particularly since her arthritis wasn't doing well on that medication anyway). Both Remicade and Humira treat both JIA and IBD so she was switched to Remicade and Methotrexate. It was also because her arthritis is fairly aggressive and was under-treated and we watched her get worse and worse. We did not want that to happen with the IBD, so we treated as aggressively as possible.
She did have granulomas on her scope, and inflammation in her colon and terminal ileum. She also has small white ulcers in her colon at diagnosis.
With Remicade, they have infusions usually every 6-8 weeks, after the initial loading doses (though they can be given as frequently as every 4 weeks). My girls did not mind the infusions - they liked missing school and getting a chance to read, nap and watch TV! Blood work can also be done at the infusions, which is very convenient.
Humira is an injection that is given every 2 weeks typically (can be given every week, if necessary). It is painful - the medication really burns, but is very convenient, since you just do it at home. Both my girls preferred Remicade, even though it was less convenient, because the Humira shot hurts.
The other option is Methotrexate - it's an immunomodulator like 6MP, but now seems to recommended more often, especially for teenage boys. It can be given as an injection or orally, as a pill. It's given every week. It does take longer than biologics to kick in usually -- Remicade is probably what would kick in the fastest.
Good luck!