Matt: Say hi to them for me will ya?
*Matt went off to the cargo bay and started practicing with the lightsaber Sir-Vin had given to him and started practicing, thinking about the rest of the group. He had mostly kept to himself, the only persons he talked to regularly were the Irvine twins.*
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.