Talk to your pediatrician about your concerns.

I am alergic to milk too, and My doctor, acually doesnt have to do a bone density test on me to cheek my calcium levels, but cheeks it through a simple blood test. If you do want to increase you sons calcium though, Silk just came out with new soy milk, and one in particular has alot of added calcium... acually more than milk its self... It has 40% of the recomended daily value of calcium.

also many fruits and vegitables have vitiman C and D in them. D is also very important to bone growth and development... Go for Dark green and leafy for vegies and usually orange and yellow for fruit. I hope this helps! Let me know if you have any more questions.