Boo. So sorry--thrush sucks. I've had some success with gentian violet, baking soda washes, and nystatin, which you might try first.
The best thing I've used, however (I have a long history with thrush, sigh), is a probiotic called Florastor (they carry it behind the counter at most pharmacies, including Walgreens and Target and also make a kid's variety). It contains a beneficial yeast called S. Boulardii, which actually removes and replaces the candida yeast. My ped. had me swab DS3's mouth with 1/2 a capsule (or 1/2 a packet of Florastor kids) 3x a day, AND had me take 1 capsule 2x a day. I did this when he had to receive IV abx at 10 days old to keep thrush away, and also to treat a case of full-blown thrush when he was 10 months.