Hmm, interesting. My main concern is whether Disney direct-to-video sequels count, because they'd be able to coattail, say, Aladdin's theatrical gangbucks with the $4.50 or so they made off the sequels from Walmart bargain bins. If we don't count theatrical releases among the series box office, I will admit I can't find evidence of a longer-running animated film series from that era, stuff like Tinker Bell and Alpha & Omega hadn't hit their stride yet.
Possible counterpoints I'd check if I weren't at work: My Little Pony, GI Joe, Transformers, Pokemon. Perhaps those mostly made their dosh off their television series and not their films?