Donnie finished doing the limos. Now he just needed a way to blow them up without risking damage to himself. He began looking for something he could use as a fuse, when he saw a row of monitors. One of them showed Meg, and one of them showed John and Tom splitting up. He recognized all of them.
The White Strikers were coming. they'd do his dirty work. He sat on the guard's chair and waited.
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.