First, have you mentioned this to the pediatrician? If you haven't I would do so, to see what he/she says.
You might want to consider making a journal. Note what he was eating, when, whether he vomited or just gagged, etc. This might help you see a pattern.
Another thing to consider is taking him to see a Gastroenterologist. They would be able to tell if maybe something is wrong with the esophagus, or if there is some kind of abnormal gag reflex.