Matt: You've gotta keep up a little faith. Let's say: IF this thing, Kira finds your sister, IF your sister can't resist it, IF it can somehow convince your sister to hurt you, IF it and your sister can somehow find us, I promise, I'll help you in any way I can to defeat Kira without hurting your sister.
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.