This is hard but HAS to be Luigi's Mansion 3 or Super Mario Odyssey, if I had to pick an older one is Super Mario Galaxy 2, the sky boxes look so good, the textures and the lighting are just peak. What you think?
idk about best looking by the usual metrics, but i wanna give a shoutout to Dream Team. I adore its 3D environments and how well the character sprites just naturally fit in them. I didn't know the game used sprites when i first saw footage of it, i thought it was genuinely 3D models. And, the way they achieved lighting and detail on the 3DS was just so satisfying. I also am fascinated by the original environments from the 2010 build of Sticker Star for this reason. It was cartoony Mario 3D but somehow had a charm that even previous console entries didn't quite match, and the HD era hits different still. And Dream Team is my personal favorite showing of those 3DS visuals, with a wonderfully unique world to explore.