*The spook comes out of hyperspace, noticing that he's somewhere not on the charts, even though it seems to be populated by a fairly modern society.*
Spook What the hell is this place?
*Before he can check more things out he's spotted, and the patroler sends a message to Duriel.*
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.