I would indulge his need to be a child, to play, to imagine, to create things with age-appropriate Legos, to swing in the park, to ride a bike, to be a friend and share.
I graduated from college with a degree in education, and when I was doing a term project that involved observing an actual kindergarten class, I met a little girl who was stunningly intelligent. She knew Latin names for plants, could spell things like tyrannosaurus, etc. She was also amazingly insightful. One day I had the assignment of working on a worksheet with her, and she got to talking. She seemed a little sad and I asked her if she was okay. She said she was sad about her little sister, who was 3. I thought perhaps the sister was ill, but my student continued by saying that her parents were already training her sister (like they did her) in spelling, in math, etc. She basically said "it would be nice to play with a ball or go for a walk but my parents won't allow it because it doesn't enhance our academic skills". Her parents did not interact with her and her sister on any level except academics. She didn't know how to jump rope or ride a bike, but she could do long division. I have never forgotten that encounter.
If your son's intellect is so advanced, sooner or later it sounds like he'll be entered into a gifted program, or you can homeschool him at an advanced pace when it's time for kindergarten or 1st grade, or you can enroll him in a virtual cyber-school that offers enhanced classes, or a faster pace for the kids who can handle that.
But in the meantime, teach him to be a child, to be a human, to play, to jump and splash in puddles, to be polite, to respect others (especially important when he'll be in social situations with children who are functioning at a more traditional 3 year old level, or with children who are developmentally delayed), to be kind, to enjoy bugs and sticks, to relax, to imagine.
Try to help him see more than the scientific or academic parts of things. If he sees a bird and knows exactly what type of bird it is and tells you "hey mom that's a black crested jay and it belongs to the crow family" or whatever, help him see another side of it. Have him close his eyes and listen to the sound the bird makes. Or pretend you are both riding on the bird's wings and pretend you can see down into the city from up in the sky.