Jokemaster: Well sir, I too regret the circumstances of meeting you, however if this hadn't happened I probably wouldn't have met you. About the Cracken siblings, you're asking the wrong guy, I don't know anything about the force and never met a jedi until recently, and I was only with the other Irvine for a short time. It was rumored by my source in Cracken's council that he had a sister, but I haven't heard from him since.
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.