Greer: Got it. This way
*Greer led them through the maitnance passages all the way to the area where Qwera worked. They managed to avoid most security guards. Finally they arrived. Greer communicated with Qwera before entering.*
Greer: Can you find some way to get everyone else out of the way?
Qwera: I can report a bomb threat, and claim to be trying to trace it while the building is evacuated.
Greer: Do it.
*He turned to Dasken*
Greer: Get ready to move in on my signal.
*Meanwhile he called Nom*
Greer: How fast can you have the prisoner ready for us to pick him up?
((And I know that you characters are on Tatooine, just don't want to have a little plot hole there))
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.