I beat Assassin's Creed III and loved every second of it. Also loved Assassin's Creed II but never finished Brotherhood or Revelations...
I've only just started Far Cry 3 but it just doesn't interest me as much, plot-wise. I do hear that it's large and open (island-based though).
Depends what you like.
At the moment, AC3 is very glitchy, has a terrible story, one dimensional characters and the poorest excuse for a lead character that gamers have ever seen. On the other hand just running around and having fun collecting things and tree-running is always awesome. At least for a while. Naval missions are the best parts of the game, so much fun. And epic.
Far Cry 3 is relatively glitchless, has an awesome story and some of the best character development of a lead ever seen. General gameplay, collecting and exploring is also amzaingly fun to just take part in. Hunting is actually fun in it and has a point.
My choice is obviously Far Cry 3. But if you don't care about the story or characters and just want an AC game in a new setting then AC3 is probably the better vote (as long as they add some patches).