One way to check for a milk intolerance would be to take him off dairy for a week (use soy milk instead of cow's milk) and then re-introduce it. When did you switch to regular milk from either breast milk or formula? I am guessing it was around 12 month of age, but if it was more recently, maybe the switch was too sudden. My son had runny poo a lot at that age, I think. Those little bodies have to do so much adjusting to new kinds of foods and some of them handle it better than others.
If you think it is food related, keep a food diary of what he eats at every meal (you should be able to get a daily menu from daycare if he is in daycare). In the food diary write down all food he eats, what time given, and what time, if any he has any reaction to it. i.e. vomiting, diareah, skin rash, etc. Once you get an idea of what food might be causing it, don't give that food for a week or two, then re-introduce it again. If he get's sick, I'd cut that food from his diet...at least for a while. Also, if you do find a food that is making him sick, read food labels carefully. You would be surprised at some of the things in certain foods. For example, a lot of bread, even plain, white, wheat or potato bread has raisin syrup in it. I never would have thought that.
Also, your husband is right, kids do vomit a lot. My future mother-in-law says "kids are always throwing up" (she has 3 grown kids, at least one of whom got carsick).
My son had a lot of vomiting spells at around that age (same age as your son). I am not sure if it was the age, or that he was at a very large daycare, or if he was adjusting to different foods in his tummy. Sometimes I could tell, and others I couldn't. I make mac'n'cheese from scratch. One time before he could have noodles (a little younger than your son), I gave him some of the cheese sauce to eat. He loved it! so I let him have a bunch, not thinking of how rich it is. A couple of hours later he vomited all over my future mother-in-law's floor (10 points for mom right there! lol). He used to poo out whole raisins, and vomited one time about 12 hours after eating cereal with pureed raisins in it...so I have not given them to him since (although he has no reaction to any bread with raisin syrup in it). IT DOES GET BETTER. After my son turned about 2 (I think it was around there) the vomiting was FAR LESS FREQUENT.
I wish I could offer help on the motion sickness front. Perhaps there is some sort of pressure point thing that is safe for toddlers? You might ask a pharmacist or perhaps a naturopath for ideas.
It is so hard knowing your little guy feels sooooo crummy. Don't be afraid to take him to the doctor for this. They will probably want to know about any kind of pattern to it (i.e. you said about every 3 weeks, so does anything stressful happen every 3 weeks). Good luck and I hope your little guy feels better soon.