I dont know whether the average caroon was better in the 90's than it is now, but i would still call the 90's a better time for animation based on the fact (or opinion, i guess) that the best stuff from the 90's was just better than the best stuff of today. Examples of this 90's cartoon greatness include:
The Disney renissance films (atleast the ones from The Little Mermaid to The Hunchback of Notre Dame). Epic, Emotional, and filled to the brim with simply MARVELOUS animation and music. Unky Walt would be proud of these films!
Ren and Stimpy. A, ahem, "childrens cartoon" unlike anything else. Probably the most insane thing ever shown on television.
Tiny Toons and Animaniacs. Probably the only post-golden age cartoons to truelly capture the essence of the best golden age short-film classics.
Cartoon Networks Cartoon Cartoons. Oh God, were do i begin to praise these masterpieces? The wacky premises, the original plots, the multi-layered jokes, the amazing direction, the great designs? Ah heck, let's just say the were flawless in every imaginable way.
Batman: TAS. The most clever and well-crafted american action cartoon of all time.
The Simpsons. Do you really need an explanation?
So yeah, 90's for me. I will admit however that with the exception of The Simpsons, the present-day Pixar films are as good as any of these things.