lantana
I think all my faves are independent decks, or were. Wild Unknown, Animal Spirit Oracle, Invisible Light, Wooden Tarot, Earthbound Oracle, Tarot of the Crone (which I await with bated breath)...
I'm in the same boat. 60% of my collection is independent (or was when I bought it), and all of my top 5 decks are indie as well. So it makes choosing kind of hard, because I feel like I'm just choosing a top deck in general.
I do love what decks like the Fountain, the Wild Unknown, and even the Prisma Visions (if you ignore how that glided cardstock tears itself up) do with their presentation and quality. Their boxes are sturdy, everything is presented beautifully, and it just feels like a wonderful package to receive.
On the other side I love decks like Slow Holler, Spirit Speak, The Collective Tarot, and countless others that bring such unique styles, worldviews, and perspectives to the tarot world that might not have been able to get published otherwise.
Not that mass-published decks can't or haven't been these things! It's just that this is what comes to mind when I think about why I love and collect these more than anything.
(I guess my answer is the Slow Holler, which is also my favorite deck in general.)