"Well, see, now that I've proved that I'm not here to kill you or anything, and you still had to test the others in case they're clones, but now I'm worried. You see, Mr. Bristow would be really pissed at me if I got tricked into giving this to the wrong person, so I'm afraid I'm going to have to ask you a few things."
Vader's wife was very pregnant when she died 19 years ago. All of a sudden a 19 year old who is very strong in the force and has a distinct resembalance to him in his younger days rolls in from Vader's home planet with his old Master Obi-Wan (Who was the ONLY other person preset at the time his wife died. And to boot, the kid's last name is Skywalker.
So in answer to your question, he knew Luke was his son because his name is Darth Vader, and not Darth Retard.
-Forum post on why Vader knew Luke was his son.