Honestly, I'm not a huge fan of either. They both possess qualities that have become annoying trends in indie films.
Aronofsky is a hack that makes simple-minded, cliched films (which are almost remakes/adaptations in the case of "Black Swan" and "The Wrestler") with really high production values and some nice acting performances.
Wes Anderson incorporates a type of douchey, hipster meta-humor in his films that I find it nauseating, and rarely makes me crack a smile.
That being said, I would choose Wes Anderson among the two. The guy is legitimately talented, annoying sense of humor or not. His ideas are fresh and original, his pacing is good, and he has a great eye for details and amusing scenes.
Most importantly, I liked "The Fantastic Mr. Fox" more than any Aronofsky film, "The Wrestler" included. (The latter was good, but not great)