I don't know your whole situation, of course - but I suspect your son would resist (and resent) any effort on your part to make him turn his back on his friends and be with you in your church.
After all, he is at the age when he is gradually "testing his wings" (so to speak) and seeking to become more independent - and painful as this often is for parents, it is a necessary stage most young people have to go through. Remember: Your goal as a parent is not to hang on to your children but to do all you can to prepare them for the day when they will be out on their own. I doubt if he is deliberately rejecting you; he is moving instead along a road that will lead eventually to adulthood.
And be thankful he still wants to go to church - even if it isn't yours. Instead of making an issue of this, let him know you love him and pray for him, and encourage him to make certain of his commitment to Jesus Christ. Then ask God to help you be a good example to him of what it means to follow Christ.
In the next few years, your son will face some of the most important decisions he will ever make, and he needs Christ's wisdom and guidance. The Bible says, "Teach me your way, O Lord, and I will walk in your truth" (Psalm 86:11).