We took my son to a naturopathic doctor when he was around 3 1/2 years (maybe 4 years) old. Up to that point I'd been taking him to doctor after doctor with no help from them. Turns out that most of my sons problems were allergies, and the ND helped sooo much, it was totally worth it. We now see a great medical doctor who mixes natural and traditional type medicine, and that works well for us.
It's definately worth looking into.
ETA: You might ask for information about food allergies for your son, if you haven't looked into that already. It can be quite common for Autistic kids to have food sensitivities, particularly Gluten and Casien (Wheat, Barley, Oats, Rye, Dairy) being the biggest problems.