I know this sounds really simplistic, but... the bible! Read to him from Genesis how God made man and woman differently, and how we are both special in our own ways. Boys and girls are both given such wonderful gifts, but they are different gifts.
We have always explained it to our kids like this... "The dad has the seed and the mom has the garden. Without a seed, a garden can't grow anything. Without a garden, the seed won't grow. But when the seed is put into the garden, it will grow!" It may sound immature, but it's an easy non-sexual way to explain it.
If you think your son is old enough to handle specifics, I think he's going to be most comfortable talking to his dad. I know my daugher gets uncomfortable when talking to her dad but she's okay talking to me. I think she can relate to me because I have the same parts as her. LOL
Good Luck!