You got some good suggestions. Great that you're going for gluten and dairy free. We are vegan, processed food and sugar free (for the most part, I slip and snack sometimes tee hee) but I've started making almond milk and my daughter loves it. You soak a cup of almonds overnight with a few pitted dates (I soak in the blender, easier) with 8 cups water. Then blend it up and strain through a cheesecloth. I bought a nut milk bag for a few $ and it's worth it. You keep squeezing and then you save the almond meal to make cookies or crackers! Does your son not like almond milk or does he react? You can easily use any nuts instead.
If you go for hemp milk, go for Pacific brand because they don't add cane juice/syrup like the others. It also tastes the best. Hemp has omegas 3,6 and 9.
For calcium go for green leafies, nori and other seaweeds and tahini.
At a year and a half why is he on formula?
Water is great and important to drink. I think it's interesting that people feel they need milk, even if it's an alternative to the cow stuff. If your son learns to drink water when thirsty, he'll be doing really well.
Unless your pediatrician has some nutritional training, I suggest you seek that advice elsewhere, they don't get nutritional training in medical school.
Good luck!