I'm sorry to hear about
your son's diagnosis. I agree with others that say he needs to be on mesalamine (probably both oral and rectal). Prednisone is not a long-term solution--it can induce remission, but he should only be on it for a short period.
Ask your insurance if they'll cover VSL #3 DS (double-strength). A lot of times the DS is covered, whereas the regular version is not. You can always try other probiotics, but VSL is typically seen as the "gold standard."
If you aren't already, I would recommend seeing a pediatric GI in a large academic hospital--they're often more experienced than someone in an independent office. If you live near any of these, I'd suggest at least getting a 2nd opinion from them:
Here are some more resources:
Support board for parents of children with IBD: