Has your son been tested for Vitamin D deficiency? Vitamin D helps the body to absorb calcium. With all the sun blocks used, it's next to impossible for the body to produce Vitamin D in the needed amounts. Only 15 minutes of exposure a day without a sun block will allow the body to produce the needed Vitamin D. If his body is deficient, your son will need to have his Vitamin D level regulated and then monitored by a physician to be sure it stays at the optimum level.
My son had foot and leg cramps at night around the same age. I gave him calcium supplements, and he would get relief and fall back to sleep. My niece suffered traumatic foot and leg pain from growth spurts. She grew 12 inches in one year in her early teens. She actually attended school in a rehabilitative hospital for children because some days she was in so much pain that she couldn't walk. She is now over 6 feet tall.
I hope this helps. If all else fails, have your son's feet examined by a pediatrist. There are some ailments of the feet that can cause this type of pain.
Let me know how you make out. Sincerely, M.