Mal headed to the ramp and began walking out. He smiled as he saw Alex's disc reader.
"He's still listening to that." He commented to Zoe.
"At least he's got headphones this time. Remember the speakers?" They both smiled as they remembered when, during the war, someone had accidently turned them all the way up while they were off. They walked up to Alex.
"Alex, nice to see you again." Said Zoe, still smiling.
"What you been up to?" Asked Mal.
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.