*Greer handed the optical disk Qwera had given him to Sellene.*
Greer: Qwera gave us this. Supposed to have locations for every ship, batallion, and squadron in the New Republic. Along with locations of suplies caches, secret shipyards, and spies. I scanned it on the ship, its clear of any viruses.
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.