*chavo gets called in*
Chavo: I got the acsess file, sir
Vice Admiral Greer: Excellent, with all the vampires running around I almost forgot about this
Greer: Long story, anyway you given any consideration to our offer
Chavo: still thinking about it sir, I got a job
Chavo: yeah, I'll give you my answer when i get back
Greer: OK, Same pay plan?
Chavo: Yes sir.
Greer: well then, anything you need, call me.
Chavo: yes, sir.
*chavo exits Greer's office*
Greer *through intercom*: send some guys to follow Chavo around town, find out who his next client is
Secretary: Yes, sir
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.