Winters walked around the scene. He looked at the window for awhile, then moved on to otherthings. He finally arrived to a crushed cabinet. He looked at it and found 2 things.
1. A giant wad of fur.
2. Drool smeared all over the wall and cabinet. Dog drool
"Vincent, you're gonna want to see this!"
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.