If you are breastfeeding, you need to treat your nipples too, in tandem with him.
I would tell your Pediatrician it is now on both sides of his mouth. And besides, you should go in for a follow-up, and Doctors usually will tell you this.
It should have subsided by now... at least with my daughter it did when she was a baby. But, I have heard that it can take awhile to go away. Try looking online...
If the Thrush is still evident in his mouth, then he still has it. Thrush is a yeast infection... oral type.
Tell your Pediatrician... and they probably will prescribe another course of treatment.
Does he also have a yeast infection/diaper rash type on his bottoms? Sometimes this also happens.
As I mentioned, if nursing, you will need to treat your nipples too... ask your Pediatrician. They should have told you this. They can recommend something for you too.
All the best,