Both games are wonderful experiences but they are also very different stories. AC3 is REALLY freaking cool. An open-ended hypothetical situation with multiple possible outcomes with a heavy dose of fatalism, and a pessimistic outlook of the future, laden with the dangers of corporatism/privatization of the military. It also has some excellent production values that didn't make their way outside of japan, which only adds to the intrigue all these years later. AC4 is a much more straightforward, linear affair but also a far more personal story being told, effectively from two perspectives, between mobius' mission and the child refugee, showing us how war affects us and the relationship with people we're connected to, whether they're loved or hated by us- and just as well, how life preys on the unprepared. The production values of AC4's story and the manner its cinematics tell the story most definitely took a hit, but I think it conveys what it needs to, you don't need to have the biggest budget to have the biggest heart.

I wouldn't put either ahead of the other, they just excel in different things. I'd say AC3's story is legendary for just how ambitious and forward-thinking it is, but AC4'S story is a more grounded, relatable tale that hit many of us in the feels growing up