I have had thrush with both newborns. Not fun.
With the first we used Nystatin. It took a while, but it did clear up.
With the second we used GSE (capsule form for me and drops in distilled water) and Gentian Violet. I also put probiotic powder on my finger and let baby suck it.
Both of those helped. Gentian violet is super messy, and I was so traumatized the first time that I turned my baby totally purple. I wouldn't really recommend it unless you're having recurrent cases (which we did have).
Turn your hot water heater up past 125. That will kill yeast on whatever you wash with hot water. Just be careful at your sinks.