Bauer signaled for the group to get down. The searchlight passed them, their backs camoflauging them. Once it had passed, the kept on going. Bauer dug a knife into one of the gaurd's neck, killing him silently. Then they seaked right below the bunker that held the MG42s, and threw two grenedes in. They quickly aimed their rifles at the door, waiting for anyone who had noticed the grenede to run out.
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.