Name: John Ryan
Bio: Parents died when he was 7. He took care of himself, but was recruited and trained by the Academy at 14.
Ryan woke up and sat straight up. He had to get to a safe place on the ship... he stood up, but fell back onto the bed. He looked around and saw that he wasn't in the ship
Ryan: Where am I?
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.