*Greer sneaked along a wall. He had made it this far without getting caught. He checked the data packet again and looked around the corner. The probe droid had rounded the corner. Quickly Greer broke into a run and started opening the hatch. Finally, he got it open and jumped in. He replaced the hatch and the Probe Droid rouned the corner back again*
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.