I voted for Lower Decks, but I do want to qualify that with the fact that I consider my "favorite" animated Star Trek show and the "best" Star Trek animated show to be two different shows. Personal preference over objective observation.
I love everything about Lower Decks-- the characters, the stories the goofiness and the so-called fan service. I can pop on any given episode at any given time and enjoy it just as much as the first time I watched it. Easily my favorite.
But, objectively, Prodigy is a better Star Trek show. It breaks new ground for the franchise, telling a different kind of story with a different kind of crew while still remaining true to the spirit of Star Trek, and managing to remain almost entirely its own thing at the same time. It is possibly, in its own way, the best Star Trek show of the new era.
That said, even when it was still available on Paramount plus, if I had to choose between rewatching one or the other, it would almost invariably be Lower Decks.
Favorite versus best.