C.,
I have a boy and girl, myself. They are almost 3 years apart (another 19 days and they would be EXACTLY 3 yrs apart). They are great friends! They go to a smallish private school and see each other often in the hallways and cafeteria at school. (They are 10 and 7). They have always been very close- best friends even. They get along with and are quite friendly with each other's friends too. I think that your kids will be close, regardless of what class they are in, if they are close to begin with. Their relationship has less to do with their class, than with their personalities and home/family life.
As for giving him the opportunity to start early, I'd say, at this age, go for it - If he is intellectually able to follow the material and able to not be a distraction to the other kids. Keep in mind, however, that emotional maturity is a big part of the class "age" during the preschool years and is definitely something to weigh heavily. You can always supplement at home for the academic growth...
One other thing I'd like to add:
If your son is as advanced as you say, and can sit for long enough to pay attention, try teaching him to read before he goes to preschool (k4). It will help you know if he can "hang" with kids with more maturity. Being able to sit still and pay attention is a HUGE obstacle for kids at his age, especially boys. "Teach Your Child to Read in 100 Easy Lessons" is what I used to teach both my kids. My son at 4 yrs, my daughter at 3.5 yrs. As for Sunday School at church, let him go where he enjoys it the most. Knowing numbers, etc isn't a big deal with what they normally are doing in Sunday School. Grasping complex abstract thoughts will eventually come into play, though. How does he fit on that "scale"?