???: Oh crap, Listen up, we're sending a Nerve gas bombing, get those guys underground.
Chavez (to gaurd): HEY, there's a nerve gas bombing coming in.
*Gaurd ignores him*
Chavez: DID YOU HEAR ME?? THERE IS A GAS BOMBING COMING IN!!
*Gaurd steadily ignores him as Chavez keeps repeating it over and over again, finally he gets tired and pulls out his comlink and calls Katori*
Gaurd: Sir prisoner is going nuts, screaming something about nerve gas bombing
*Chavez is heard in the background still warning them*
Gaurd: Requesting orders
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.