Daiya is sold at whole foods and is soy and casein free.
For other protein:
Whole-fat coconut milk (the best is Native Forest canned- it's only coconut milk and in a BPA-free can) This is great in smoothies and most baking. Rice milk, hemp milk, and nut milks work too.
Soaked and blended raw cashews can sub for cheese or top cupcakes, depending on what you mix with it (there is a recipe on my blog for queso:
www.chickiepea.wordpress.com -- look under recipes) and you can make a chevre' cheese with cashews too (www.veganjoy.blogspot.com)
Organic extra-virgin coconut oil
Ghee/clarified butter sometimes works because it doesn't contain the casein protein
Lentils
Beans
Lots of greens (I find that if I dehydrate them, I can powder them and put them in anything and my kids don't realize it. Otherwise, they don't eat salads, etc.)
Hummus is a good one for adding a creamy texture. I make salad dressings with mayo
Woodman's has a great natural aisle with dairy and soy free items (frozen, etc) and vegetarian/vegan meals. They are cheaper than Whole Foods and have different options. I would check Trader Joe's too, and even Dominick's. They all carry various brands and have different prices, so shop around!
I would start browsing the vegan and raw websites, even though you are not vegan. There are lots of good ideas on those sites about how to work around not having dairy products, and most people are realizing that soy is really unhealthy and avoiding that anyway.
It's also good to look up names for dairy that you might not know. It can be hidden in lots of things (especially bread.) When I had to go dairy-free while breastfeeding my youngest daughter, I learned the kosher symbols on food since they indicate dairy-free (very useful!!)
He may tolerate goat milk and cheese, like someone mentioned, or even sheep or buffalo. My daughter is 3 now and she didn't tolerate dairy at all, or so we thought (she reacted to breast-milk once when I licked ranch dressing off my finger!!), but as it turns out, she tolerates raw (unpasteurized) cow milk just fine. There are several dairies in the area where you can buy milk straight from the cow if you want to test this theory (assuming his is not a respiratory or very severe reaction, of course!)
Hope this helps!
M.