*a sniper rifle sticks out a window from where Flax is running, it aims at the probe droid. It fires one EMP pulse, and hits the probe droid. The probe droid stops momentarily, but continues chasing Flax*
Sniper: Damn *Calls greer on the comlink* Probe droid still chasing target.
Ackbar Memorial Hostpital, Corusant
*some time after Rwos left.*
Greer *through comlink*: Keep him in sight, don't let any harm get to him. I have a feeling trouble is brewing.
*Greer turned to the news on his datapad. Another great general had mysteriously died. Greer sighed, most of the good leaders had died in some other mysterious way. If Flax died he didn't know if there would be enough leaders left. He turned to Gilan*'
Greer: Any change?
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.