My baby has a cough that causes him to choke...?

My baby is 2 1/2 months old and has devolped a cough to the point that he gets to coughing and starts to choke. This happens randomley and in the middle of feedings (sometimes coughing up his formula). The doc. put him on zantac liqued for acid reflux, but it doesn't seem to be getting better. He will wake himself up choking and then he strats to cry like he is in pain. Could it be acid reflux or something else?