Suddenly a figure landed silently behind Charlie 34. The man quickly grabbed him and broke his neck, in a blink he jumped up, kicked 78 in the head, and grabbed the blaster. He pointed it at his face.
"How many of you are there here?"
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.