Hi J.,
You can try the goat's milk, but many children who are sensitive to cows' milk are also sensitive to all other forms of commonly available mammalian milks (like sheep). The exception to this is camel's milk, but I think you're going to have a really tough time finding that in the US. I don't even think you'd be likely to find it in a middle-eastern market. BTW, if you decide to try the goat's milk route, do NOT get it raw, as suggested by a mom below. The risk of your son contracting a serious Listeria or Clostridium infection is too high. Pasteurization does not destroy the important proteins and sugars in the milk -- it only kills the bacteria that can cause disease. Even if some proteins were minimally denatured, the amino acids constructing them would remain. It is the amino acids that we need to consume for nourishment, not the proteins (which is why formulas like Neocate and Allimentum are useful). Proteins are digested into their component amino acids in the stomach and small intestine, any way. I do wish people would learn a little Organic Chemistry, Biochemistry, Food Science, and basic Physiology before posting dietary advice here! (My areas of expertise are in Molecular Biology, Immunology/Allergy, and Infectious Disease.)
There are a number of other milks you can try, such as hemp milk (as the GI specialist if it contains enough nutrients for a toddler), and soy milk. A lot of kids with milk sensitivities are also sensitive or allergic to soy, however. Talk to his doctor about a good multivitamin to bridge his nutritional gap. Be careful about using many of the over-the-counter brands, though, because they're often prepared in a milk base. I know there's adult dairy free vitamin, Nutrient 950, which is very good (this the only multivitamin recommended by my son's doctor for him, since he has Crohn's disease and must stay dairy and gluten free).
Most kids are pretty good about not starving themselves. If you have to wean from the Neocate, it may take a while and be very nerve-wracking to you, but you may find that your picky eater will expand his diet and eat more solid foods to satisfy the needs of his body. You can also try to hide nutrient-rich foods in the foods he will eat. I used to puree all sorts of green vegetables and sweet fruits together (like apricots and watermelon), and make my own fruit roll-ups using a food dehydrator. The kids loved the taste of these, and never even knew they were eating veges. I also found that the kids would eat just about anything if I cut it into fun shapes, so I kept a stock of cookie cutters in various shapes and sizes. It's a bit more work, but pays off in nutrition. I also found that my kids would eat things if they helped to prepare them, and started them cooking simple things in the kitchen with me when they were about 2 years old. I would let them do things like mash cooled potatoes, stir eggs, push the button on the blender, etc. They loved it, and both became pretty accomplished cooks by the time they were 6 - 7 years old (their now 21and 18, and cook better than I do!).
If you really need to keep him on the Neocate for adequate nutrition, perhaps you can get the GI specialist to address the issue with the insurance company under the terms of medical necessity.
Good luck! The good news is, the vast majority of toddlers who are allergic to milk outgrow the allergy by the early childhood years. Hopefully, this will be the case for your son.