Matt: Sorry. Too used to talking to people who have been here for everything. A couple of weeks ago we were on the Aesir's home planet. We had to do a couple of things that would take a while to explain, basically get a key or something, then fight in a battle if we wanted to, but anyway, midway to or from getting the key, I don't remember which, we were attacked by a couple of people and a lot of strange creatures. They were after Guy, you're probably about to meet him, so he'll be able to explain things a bit more clearly than me.
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.