I am so sorry... My son and I had thrush when I had him 17 months ago and it was AWFUL... It ruined breastfeeding for me..
First- Nystatin didn't work for us... It took two rounds and two pediatricians before I could get my son what he really needed. (Diflucan) If you look at the directions for Nystatin it says "Gargle, swish... keep in your mouth as long as possible." Yeah right... try that with a 5 week old... :) Diflucan will knock the yeast right out of both of you, but you both have to be treated. Keep pestering the pediatrician over the phone and tell them the Nystatin is not working. Even if you have to try different pediatricians... that's the one that will work.
I did try Gentian Violet, an old natural remedy where you paint this bright blue/purple stuff in your baby's mouth. However, as soon as I did it I panicked and called poison control... He looked like the Joker! I was told it was alright, but it was still scary...
I went to Whole Foods and bought every single thing I could find... Coconut oil.........grape seed extract.. any kind of natural anti-fungal remedy I could find... I would paint my nipples with so much stuff... but we just kept passing yeast back and forth... I had a C-section and they just pump your body with so much antibiotics that your body kills off the good bacteria... You could probably try a probiotic for the both of you.
Also- I got this pamplet from the lactation consultant about other things like washing ALL linens, sheets, and towels every day.. Eliminating sugar and carbs from your diet.......... (for you and EVERYONE in the house) As a first time Mom, I was lucky I was eating or washing anything, let alone doing it every day without sugar. It just wasn't going to happen...
One thing that did really help was a microwave sterilizer. I could sterilize the bottles and pacifiers after each use with very little effort. And- Vagisil antifungal cream helped with my son's SERIOUS diaper rash. (The stuff the doctor gave us made him bleed and did not help, but over-the-counter Vagisil cream worked)
I wish you the best of luck. I wouldn't wish thrush on anyone! They don't really tell you about it in the baby books or in the hospital... Now I know what to look for...