*Perez patched Qwera over to Greer*
Qwera: Why didn't you tell me about the people taking over the Republic?
Greer: I was pressed for time.
Qwera: Forget that. I want an extraction.
Greer: In return for what? We aren't exactly about to spare agents just to extract coworkers.
Qwera: I have valuable information. Something that's probably vital if you want to win the war.
Greer: Concerning what?
Greer: Keep talking.
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.