Could be reflux, allergies, asthma, or combination...or just coincidental and it's a virus. It is possible to have a milk allergy and only respond at night. The milk allergy part can be causing reflux. Is he only getting milk at night? Other symptoms? when the vomiting starts, is it always 2 hrs after? Has it happened more than once? If so, it could be FPIES - Food Protein Induced Enterocolitis Syndrome to milk (my dd has - to milk). That's a non-ige reaction - so not "typical" allergy sx, but vomiting/diarrhea 2 or so hours after ingestion.
Keep a food log and see what happens w/ foods, reactions, times happening etc.
go to www.kidswithfoodallergies.org - tons of info and you can ask for help and support
look at my previous food allergy posts - there's a lot of info in there too
talk to your dr, but as pp said, not all are up on food allergies, especially Non- IgE reactions. Contact a pediatric allergist - we go to Children's Memorial at the glenview annex. 800-kids-doc