*Elella's yell pulled Matt back into conciousness. He opened his eyes*
Matt: I'm OK. *He stood up, wobbled a little bit, then collapsed again*
Dammit. Why'd it weaken me so much this time? With my brothers it was fine. Maybe we're too far away....
Matt: Guess I'm not that well.
*He sat up, but it seemed to be the most he could manage. He wondered if his effort did more ill than good*
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.