Hi - My Baby Has Had Trouble Eating Since He

Hi - my baby has had trouble eating since he was 6 weeks old ( he is 4 mo). He gags and coughs when he starts, and usually gulps a few swallows before giving up. He's a happy boy except when he's tired and wants to eat and sleep (and he can't). He has been treated for thrush for a week and half, and it's starting to go away (I'm on treatment too). Yesterday he was so happy and are well so I thought that we had fixed it, but today he is back to his old self. Could his throat be swelling from a food allergy?? We tried reflux meds but it actually made it worse.