It depends. तुम is intermediate in formality between तू and आप. So, the given sentence would not be considered impolite if you were talking to someone who is around the same age as you or younger.
However, if you are addressing someone who is significantly older than you, in a position of authority or is a stranger who you want to be very formal with, you would say क्या वह आपका बेटा है?
If you want to tack on some formality to the son as well (if you are a teenager talking to an old lady about her adult son for instance), you would say क्या वे आपके बेटे हैं?