Logan stood up and led her to Mike's desk. He was speaking on two phones at once and typing on the computer. He saw Logan approaching, and recognized Teri. He signaled for them to wait. He seemed to be arguing with two people at once. Finally he hung up.
"Yeah, what's going on?"
The day of the attack a small group of people met in a garage. They all wore some green item of clothing
"All right, everyone ready?"
"Know who the target is?"
"All right. Let's get rolling."
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.