There are many calcium and vitamin D fortified non-dairy drinks available. Many are sweetened with brown rice syrup and other non-corn products. They are also very tasty, delicious alone or on cereal. You can find your biggest selection of these drinks in a health food store. Although they may be in the refrigerated section, they are shelf stable and are usually found in the aisles.
Milk is often a significant source of protein in an toddler's diet.
Since your son is not drinking milk or eating dairy foods, be sure you include other protein rich foods in his diet. Some meat or fish, or legume grain combinations are good. Also include eggs and nut butters. Having your son drink water for thirst is great habit to cultivate. However, serving more juice than 4 to 6 ounces a day is not.