*gaurd wakes Chavo up*
Gaurd: weve arrived.
Chavo: Can i get prepared at least?
Gaurd: you have 5 minutes
*chavo takes out a piece of old fashioned paper and pen. i which he writes:
Ive seen you following me, are you gonna help me or not? then he proceeds to get ready*
Gaurd: 5 minutes are up
*on the way out he drops and kicks the paper twoards the suspicious engineer*
*arrives at council building*
Gaurd: were waiting till the meeting is almost over
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.