Could be the post nasal drip. If it's really thick mucous, have you tried childrens Mucinex to help break it up? They make it in a dissolvable flavored powder now too.
I'd also make an appointment with an allergist, and by-pass his pediatrician completely. My pediatrician didn't think my son had any issues with his tonsils...but he was snoring while awake & vomiting because his gag reflex was so sensitive due to his tonsils constantly touching each other! I made an appointment with an ENT, and turns out his tonsils & adenoids had to come out. Moms have an instinct, sometimes you have to act on it.
Also, i don't know if this is remotely in the ballpark of why he's vomiting, but has he been tested for cystic fibrosis? I know with that affliction it produces thick mucous in the lungs. Children with that also are known to have a productive cough & very salty skin. you can look up the symptoms online & see if anything sounds familiar. Just good to have all your bases covered! Good luck mama!