((Scar: My character that's working on the Star Destroyer hears everything Chavez hears, that means he knows there was a probe droid near there, he knows Chavez is hanging outside captured. When he finds out about Nerve Gas bombs, he takes a chance and warns Chavez. He isn't exactly sure about where the bombs are going, but he wants Chavez to get to safety just in case.))
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.