Grapefruit seed extract is an antimicrobial that is recommended by both Dr. Newman and Dr. Gordon for application to nipples with thrush (diluted though), and Dr. Gordon says you can use the diluted solution in the baby's mouth. I used it with my LO when she was about 3 months old, and though she made a face when I swabbed it in her mouth, it was otherwise fine. Just follow the directions in the links above
I got both the GSE and the probiotics at a health/supplement store. I guess it depends on where you are as to what's available, but I'm sure you could find it online. I did order baby probiotics (hmf natogen), but you can just use an adult capsule - break it open, put the powder on your finger/nipple and give to baby.