*Chavo's ship exits hyperspace*
Chavo *seeing what happened*: Oh crap.
Chavo's ship: Heat alert, heat alert, reaching maximum hull tempareture.
Chavo: Double crap. Gotta get out of here quickly.
*Chavo plots a hyperspace route back to corusant, and goes into hyperspace again
*The spook sent to track chavo bangs on the walls*
Spook: AREN'T YOU GONNA INTEROGATE ME, ASK ME QUESTIONS, SET ME FREE, HOLD A TRIAL ANYYTHING?
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.