As long as you wash them they are just fine. I have never heard that it was bad your the baby before. In fact the skin is the best part it holds most of the vitamins and nutrients of the Apple.
Apples are commonly grown using the highest amount of pesticides that can collect in the skin. In order for farmers to produce a healthy crop that are presentable and not bug eaten they use a ton of chemicals. Peel them or buy organic. I know a bit about this because I juice my fruits and veggies.
Baby brothers! Lol they know everything. At least mine does.