My son was diagnosed with GERD at 2 months and still has it now at 26 months. I was and continue to be nervous about the medications and especially the lack of research on how they might affect kids, especially long-term. However, I have to be honest in saying that the prilosec and then prevacid have made such a difference for him that I absolutely believe he would be a very different kid, both emotionally and physically without it. When he was a baby he would scream in pain but now (without meds) he coughs all night long and basically aspirates from the reflux - regardless of how long ago he ate, what he ate, how he is positioned, etc. My personal opinion is to not worry too much about the medication for the short term but, if things stabilize for your son and he seems to be moving in the right direction, seriously consider some of the more natural remedies. It seems that his failure to thrive diagnosis means that you've got to treat whatever you can pretty aggressively and quickly.
I agree that you should be ruling out food-allergies, it's easy enough to ask and get tested for other things while still treating for reflux. My understanding is that allergies are pretty often diagnosed as reflux.
Reflux often goes hand-in-hand with other issues such as ear infections, allergies, athsma, and sinus infections. My son had ear tubes at 14 months and uses a nebulizer whenever he gets a cold.
There's a lot of stuff online - both regarding GERD as well as the medications. www.infantrefluxdisease.org has great message boards for everything GERD related as well as diagnoses that often are related. We also have a pediatric gastroenterologist and I definitely recommend getting a referral to one if you do find out it's reflux - while still balancing that with non-medical opinions like chiropractors or herbalists.
Good luck and hang in there!