*sees the an R-41s lifting off with Kioet at the controls*
"looks like they're gone now"
Chavo*to gaurd*:I have to go"
Gaurd: I guess it HAS been a long time. (to stormtrooper) escort him
*arrive at an old-fashioned bathroom with the stall doors opening to the outside*
*enters stall, and stands out of view*
stormtrooper: you done?
*knocks urgently at the door*
stormtrooper: better check it out
*opens door so hard it knocks the stormtrooper out*
Chavo: oldest trick in the book
*steals stormtrooper uniform and walks calmly out*
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.