*Greer went to the cockpit and checked their location. The pilot ignored him. He walked back*
Greer: OK, we'll be dropping out of hyperspace soon. Get ready to leave. Perez, I want you to be ready to contact Qwera through any means once we arrive. This should be simple, we walk in, contact her, walk out.
*Finally, the ship dropped out of hyperspace and headed toward Corusant, ready to land.*
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.