In the new version, the Emperor tells Vader that the one who destroyed the Death Star was, in fact, "the offspring of Anakin Skywalker," to which Vader acts confused, because Vader was under the impression that Anakin's child had died with his mother. This has led to some confusion, because earlier in the movie, Vader specifically searches for Luke Skywalker and already should have known that he was Anakin's son, though it is not impossible to think that perhaps some people around the galaxy would have the same last name and not be related. There were actually characters named "Bail Antilles" (merely mentioned in The Phantom Menace) and "Captain Antilles" (from Star Wars and the previous owner of R2-D2 and C-3PO). Also, the character "Wedge Antilles" is one of Luke's Rebel friends and a fighter pilot who appears in all three films of the original trilogy. None of these characters are ever suggested to have been related. The original scene can be viewed here.
However, another possible reason why Vader is surprised to hear that Anakin Skywalker has a son is that he merely acts surprised to foil the Emperor. Following the destruction of the Death Star, Vader found out the identity of the rebel who was responsible. The name coupled with the boy's strong connection to the Force was probably enough to identify Luke as his son (Vader later tells Luke to "search his feelings" for confirmation that Vader is his father as well). As Vader reveals later on, he plots to overthrow the Emperor, and he believes he needs Luke's help to do this. To keep this plot secret, he also kept his knowledge of Luke's existence from the Emperor; suddenly admitting to the Emperor that he already knew that he had a son would be most suspicious in the eyes of the Emperor, so Vader may therefore act like this information is completely new to him. This is a scheme often employed by Sith Lords, as in Attack of the Clones, Count Dooku also acted surprised in front of the Separatists at the news that the Jedi had a Clone army, yet later it became perfectly clear that it was he himself who had ordered the creation of the army; "lies, deceit and creating distrust" are the ways of the Sith, as Yoda pointed out.
According to the canon Marvel Star Wars and Darth Vader comic series, Vader did indeed know that Luke was his son prior to the events of The Empire Strikes Back. This is further supported by the fact that the opening crawl text says he is searching for "Young Skywalker."