Ohhh~
This would be a pretty fun battle to watch. In term of pure swordplay, Vader has this in the bag. Not only his experience is greater, but he algo geared his fighting style to compensate for weaknesses. This is not discrediting Link. I think he can adapt and potentially even out-manuevering Vader a couple of times, but Vader simply has the best combat feats of the two.
The problem comes from the arena they are fighting in. The Halbert. While Link's arsenal is certainly deadly for Vader (Focus Spirit Gauntlets and Spinner comes to mind with their AoE electric attacks), if Vader times his attacks right (and probably should, thanks to precog) he could go for a good ol Force Push on Link and throw him out of the Halbert.
That said... The Fairies and/or Hookshot could get Link back on to the ship, but I mean... A Lightsaber could probably cut through the hook, so that option is limited to a one time only.
Another problem for Link is the fact that Vader uses his telepathy to enhance his swordplay. Yes, Link has a resistance to mindhax, but Vader could still percieve Luke's thoughts during their duel on top of the Death Star, taunting him when he got the information about Leia. In that specific instance it backfired, of course, and this probably wouldn't affect Link that much, but the fact that he could learn info through that remains.
The Great Fairy's attack (dropping Majora's Moon) is extreme, and I could see Link gaining an advantage through that, since they are in such a limited space. Even if Vader tried to stop it through telekinesis, it would take considerable efort from his part and through that Link spamming electric attacks would eventually cripple Vader.
But there is still a problem. Vader can survive without the armor.
Is a matter of if Link can do the exact stuff to win, and do it before Vader figures him out through telepathy and precog.
As such... Vader probably has the advantage in combat. Spinner and Gauntlet is pretty good, but for it to do an AoE Link has to stomp the ground. Vader could stop the stomp with telekinesis and go for a Saber Throw. Of course, Link could retaliate with bow and/or bombs, but I think it just too specific scenarios for Link.
All in all, Vader has the exact tools to take out Link... Without even counting Force Choke. (Though Link could escape summoning the Fairies)