Name: Eddie Shannon
Occupation: Jedi Apprentice
Bio: A thief who was recently found stowing away on a jedi ship. His force-sensitivity was discovered and he is being exchanged from master to master until they can find a permanent one for him. He has volunteered for this mission to have a chance at proving himself. Usually reckless and daring.
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.