If your dr okays it, there's acidophilus for babys at Whole Foods and similar stores. Baby-dophilus is one brand.

There's also Gentian Violet, which REALLY kicks thrush's ass. I had systemic thrush for about a year, did Diflucan, etc. What finally worked was GV. Screaming pain to cleared up in three days, and didn't come back for months. I finally went on a low carb diet and that got rid of it for good. Not practical for an infant, but the GV works like a charm. There are possible issues with side effects though, so investigate, obviously. I'm not a medical professional. And the GV stains everything it comes in contact with a lovely deep purple.