Expect Janna to make this thread :p
A hard questions for sure. I have a long list of Pokemon that I find super cute, but picking a top 3 between them isn't easy. I can for sure say that Teddiursa is probably my favourite cute Pokemon, something that's been the case probably ever since I saw it in the 3rd Pokemon movie.
I'd also say that my playthrough of Let's Go Eevee has elevated the titular Pokemon up there. I've always found Eevee cute, but the canonicalization of its cry from the anime just gave another dimension to it. Since Eevee has been a lot less of a mainstay in the anime, I was never too familiar with the cry, but it grew on me very quickly. Maybe it's just recency bias due to a bit of a hiatus from the Pokemon franchise, but I'd say for the moment, Eevee is definitely top 3.
As for the third one, I really can't say. There are so many Pokemon I find equally cute, and I just have too hard a time picking between them, so I ended up resorting to just looking through a list of all the Pokemon sprites, and going with the one I found to be the cutest. So as for now, my third one would have to be Azurill. Aside from just having the standard cute looks that a lot of the baby Pokemon do, I feel like the helplessness it portrays also adds an extra layer to it, so it just ended up really catching my eye.
Tl;dr
Up for a lot of debate, but as for the moment, I'd say my top 3 is Teddiursa, Eevee and Azurill.