They're all excellent.
Classic Disney and Pixar were both eras of innovation. Disney took a medium which was good for 10 minute, silent, black and white films only a decade earlier, and turned it into something that could produce a full color movie with detailed sound. Give it only a few more years, and they invent surround sound (it was used a few times for Fantasia showings). And these movies were actually really good.
Pixar did more or less the same thing. CGI was good for short films and maybe some low-res effects (see: Tron) and made movies of it. Again, the movies were really good.
That said, I think the "Disney Renaissance" might have a slight edge over classic Disney, only because it was a little more than 5 years of near perfection. The Lion King is probably my favorite animated movie ever, and the other movies of the era were excellent. Not that 30's-40's Disney was bad, but there were a few not so great movies in the same mix as Snow White, Fantasia, Pinocchio, and Bambi. Stretch to the 50's and you have maybe 8 really good movies in 15 years, vs. 4 really good movies in 5.
Like before, the same goes for Pixar. Ratatoullie, Wall-E, and Up are just an insane streak of excellence (and Toy Story 3 is the best in the franchise, in my opinion). Same as before, Toy Story and Monsters, Inc. are still great movies, but Wall-E and Up are two of the best works of animation ever, and nothing from the early Pixar era can match those movies on a quality standpoint.
It's really hard to choose. You can take one of the two most innovative periods in animation or one of the two highest quality periods in animation. I think that early Disney bests early Pixar (this is what launched the medium, after all), but 2007-2010 Pixar is better than 1989-1994 Disney (Ratatoullie + Wall-E + Up + Toy Story 3 > Little Mermaid + Aladdin + Beauty and the Beast + Lion King). Beyond that, I can't make a decision.