• "You are handsome, but your son is more handsome than you."
• "You are ugly, but your son is handsome."
• "Your son must have gone his good looks from his mom, because he surely could not have gotten them from you."
• "You and your son are very handsome, and you imparted your best qualities to him."
• A throw-away comment that means absolutely nothing.

So, which one is it? 

I asked a Korean what it means to a Korean.

Actually,  to Koreans, this utterance is a throw-away comment, something Koreans say to fathers with cute kids.  It’s intended to be small talk, not a referendum on the child’s looks or the father’s appearance.

Now how would a native English speaker interpret that comment?

I may be wrong, but I believe most English speakers would find the comment a bit negative.  Akin to the Chinese comment frequently uttered about people’s weight, "You look fat," (which in its purest sense means you look healthy, not fat), "Your son is more handsome than you" is the kind of comment that can be easily misinterpreted in English.  If you are a narcissist, you might assume that it means you are handsome and have great genes.  If you have self-esteem issues and/or are self-deprecating, you would probably take it to mean that you are ugly while your son is handsome.