Infant Reflux- 12 weeks old

I have a 12 week old son who has been on a downward spiral in his eating. He used to be a great eater up until 7 or 8 weeks and it has progressively gotten worse and for the past week he has refused my breast and the bottle. He screams and whines. We have to "trick" him to eat usually and then he pops off and is definitely uncomfortable. Doctor put him on Zantac a few weeks ago and then we tried Prevacid for three days this week but it wasn't helping and we would rather not give our baby medicine so we are looking for any remedies. We stopped meds Prevacid two days ago and Zantac over a week ago and nothing is better. He is probably taking in about a third of the ounces he should be getting each day. He also hasn't pooped consistently, which is way out of the ordinary for him. About once every two-three days now.

I have read about the Nat-Phos treatment but am open to other ideas and suggestions on how to proceed. We just want our happy little eater back.