Hi E.,
My daughter had thrush at 2 weeks and it lasted until about 8 or 9 weeks. I believe that she got it because I was on IV antiobiotics for about 9 hours during birth. Antoboitics kill our beneficial bacteria that protect us from bad bacteria like thrush.
I took orally and rubbed on her toungue acidophilous after 3 weeks of the meds for her and I not doing anything. Since you are breast feeding you should daily take acidophilous or some sort of prociotics to build up his benefical bacteria. Also drink a shot of apple cider vinegar every day to combat it.
I also washed my nipples with vinegar- if I were you I would do that with anything he puts his mouth on.
good luck that is a nasty thing to deal with!!!!