Damn, tough choice here. I think I have to go with Ghibli, but it's essentially two studios as perfect as they can possibly be.
The Incredibles, Coco, and Up are my gold standard for Pixar and Western animation. I haven't seen Wall-E, Ratatouille, or Inside and I hear those are all contenders for their best films. I think the Toy Story franchise is massively overrated, though groundbreaking and massively influential.
Ghibli is harder to nail down because despite there being similar themes of freedom and self discovery, the tone and subject can be massively different for every movie. Princess Mononoke and Spirited Away are perfection. Ponyo and the Wind Rises were damn close. My wife really enjoyed Kiki's Delivery Service because she could relate so well despite finding animation and Japanese culture completely unrelatable. There's more movies that I would love to see and just haven't been able to yet, but I have noticed fans seem to have a wide range of favorites in the catalogue.
I think my two favorite films from each studio weigh evenly with eachother, they both have many very good movies beneath them. But the lowlights might make a difference. Ghibli has done smaller experimental stuff that's been passable but not exceptional. But Pixar has Cars and that docks a point or two.