AC 3 if you like stealthier/sandbox games, Far Cry 3 if you like first person games that are very open ended (think skyrim or fallout).
I just recently got the platinum trophy for AC3; however, never played Far Cry but I've heard good things. Both are great games, I know that AC 3 has DLC out and more on the way, on top of the fact they have a "smoothing out" patch to be released very soon.
Like I said, I've heard lots of good things about Far Cry, I haven't played it though. I know that there are a lot of "random events" in Far Cry, much like the first fallout game. For instance, you're doing your normal thing running for point A to B and on the way you see a deer run past you, then a few seconds later a pack of wolves ... then a few seconds later a group of guys chasing the wolves.
Both are great games, it really depends if you prefer first person(FC) or third person(AC), sand-box(AC) or open-ended(FC).
Having played assassins 3 on wiiU and Far cry 3 on ps3, i can say, far cry 3 wins. Assassins has better graphics and less glitches, in fact Far cry 3's screen tearing is very annoying as is the framerate, really terrible performance. BUT, for the first 7 hours or so of assassins, half of the game is cutscenes, most of the game plays by itself, only later on it gets better. On far cry, 99% of the game is game. This reason alone makes me choose far cry 3 as the best of the 2.
Far cry 3 is more of a fun game, assassins is more of a serious game, consider it if you enjoy american history. Assassins is a bit more varied, with winter/summer changing the look of the world, also the rain is the most beautiful ive ever seen on a game. The sea missions are the biggest thing for me gaming wise this year. Far cry 3 all the places look the same but the game is so much fun. Far cry 3 has the most beautifull fire i've seen on a videogame and almost everything can be burnt.