I wanted to add that there is a great trick for applying Gentian Violet (if you choose to go that route...or for anyone else who is interested). This method was perfected by some lactation nurses I know: apply a liberal amount of petroleum jelly to the outside of your son's mouth, including the outside of his lips and his cheeks. The Violet will not dye the areas with the jelly. Also have him out of clothes altogether, and you should probably remove your shirt too because this stuff is incredibly messy! Place a Q-tip into the Gentian Violet and kind of push it against the top of the bottle to remove the excess. Just rub it in your son's mouth, being very careful not to touch the Q-tip anywhere else. That's it. Throw away that Q-tip and wipe off the petroleum jelly. I would dress your son in something that you don't mind getting stained. I never got the Gentian Violet anywhere on the outside of my son's mouth but it still managed to stain the collar of his pajama's (I always did the application right before bed; I just washed the same pajamas every day.) If you are breastfeeding, put some Gentian Violet on your nipples as well. Repeat these steps for 3-4 days, with only one dose per day.
Nystatin is so overused that it is only effective in 30% of yeast cases, and it's possible that those cases would have cleared up on their own anyway. Diflucan is much more effective, for sure, but so is Gentian Violet and it costs less than two dollars and requires no doctor visit.
Anyway, hope some of that helps. Before you do anything, though, you should call your doctor, just to be safe.