*Matt finally got tired of practicing and went out. The halls were almost abandoned, and with a sense nearing dread he walked along them, until he finally saw Tanara and a girl he assumed was the sister she told him about. He approached them.*
Matt: Looks like I was wrong. She did manage to find us. I assume everything is OK now?
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.