Meanwhile in the Black Destroyers' garage, Donnie had wiped out most of the guards. The rest were retreating until backup arrived. He quickly began searching for something to help him blow up the limos. He didn't just want to blow them up, he wanted to make a statement with them. He looked in the supply closet, and grinned. He'd found his thing.
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.