Aside from judging films' legacies on others or box office numbers, I suppose the criteria for judging the "best" of anything is subjective. That being said, personally I would argue for Who Framed Roger Rabbit, which admittedly is partially animated with mostly live-action sequences. The opening for the movie alone is just hysterical beyond words, to say nothing of Bob Hoskins' and Christopher Lloyd's utterly fantastic performances.
I just think it's the wittiest and funniest of the whole bunch from that decade. The gritty language and subject matter is also mature enough for grownups to watch too. Strong runner-ups include My Neighbor Totoro, Brave Little Toaster, and of course The Little Mermaid. Perhaps you think one of these or a different flick altogether is more deserving of the title?