The young boy had stayed silent. Now that the Jedi were gone he quickly took out a small sensor and checked himself. No kind of tracking device. That was good. He then took off running. One gaurd saw him running and chased after him, which caused more gaurds to come running after him. He quickly ran to the garden, jumping over Rebecca and Shade, with the gaurds chasing him
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.