HUGS, mama! It is NOT your fault! I hope the thyroid study shows that your thyroid is back to normal, but if not, you did the best you could. I'm thinking methimazole is incompatible w/ bf, right? I have to pill my cat and I get paranoid about washing my hands!
Kids get sick - even breast fed kids. My 13 month old breast feeds and she has croup! And her 2 year old brother has the tail end of a cold - and HE was on formula from 3 months. You'd think HE would be the one with croup, but no.
Also, I was on formula from day one and had a couple of years of ear infections, no biggie. My sister at least got colostrum, but she was also ff. She needed tubes in her ears. It's more about anatomy than mom's antibodies. My daughter has caught every cold her brother has this year, even with bf. Hers were generally mild (until now) but she still got sick. If your son has weird eustachian tubes, he'll get ear infections a lot - but that would be true even WITH bf. HUGS!