Honestly? I think 3&K and Mania are on par. The first half of Mania (culminating in the Metal Sonic fight) is probably the greatest stretch of game in the entire series. But then on the other hand, everything from Lava Reef onwards in S3&K is bonafide platforming greatness.
I think I'd probably lean towards Mania even in spite of it's zone reuse because it's level gimmicks tow the line between "fun" and "overstays it's welcome" a bit more consistently than S3&K.
Overall Sonic Mania, but 3 & Knuckles is a close second.
I agree with Dusk in that S3K does the cutscenes better and feels more consistent overall. Like, there's no moment to be found in Mania that felt as impressive as the interactive cutscene in hidden palace
Sonic Mania does the best it can to bring all the classics together into one package though. The overall mechanics are refined, level collision feels more polished, rolling up into a ball feels more reliable because of that. The remixed stages all ended up being more enjoyable and interesting for me. The elemental shields interacting with the environment is awesome and should be expanded on further. Drop dash is great.
The soundtrack in both games.. damn, just fantastic stuff. I was never a fan of CD's JP/EU soundtrack but absolutely love the Mania tracks for those stages.
To build a bit more off of this, Angel Island often gets shifted when it comes to talk of good first Sonic levels, but the shift from tropical paradise to the place ravaged with fire and then being bombed on all has a certain feel to it which I find appealing. And of course, the end of Sonic & Knuckles from Lava Reef to Doomsday just has some amazing build-up and interconnected final-ness that gives both a certain feeling and coherence naturally told in the levels which I think is also unmatched in the series. There's a great build-up and execution between Lava Reef, Hidden Palace, Sky Sanctuary, Death Egg & Doomsday which I honestly don't think the series has ever been able to match, and I don't think Mania matches it either, but it completely exemplifies the best parts of Sonic 3 & Knuckles world building and storytelling through level design and subtle details included with a certain atmosphere it emits.
However, Mania does have a benefit that some of its best stages are among the best in the series(though not all are winners I feel), I do think it gets points for how many ideas is on display. Sonic 3 & Knuckles has a few week points in levels and sections as well, but I do think there's a charm to how it builds off it's stage-to-stage mechanics. Mania has more and overall I prefer it, but it could also be argued it in some ways has
too many mechanics in each level. I don't really hold that as a negative, but sometimes it does feel like there's a lot going on in each stage.
Anyways, Mania had to balance being the team's first original game with all of them together while also being sorta' a love letter to the classic series and having mostly revisited stages. I think it's very, very good for what it is. Though I hope the team gets an opportunity and takes it to make an original game with it's own story, one thing I am under the impression of is they've probably learned a few things from Mania, and if allowed creative freedom to just do their own original levels and story, it could end up being a top tier Sonic game unquestionably. And some of what S3&K has over Mania I think comes to its world building, but Mania was always made to be a game of returning stages so it'd obviously have a harder time than a game which is set in one location (though admittedly that location is stretched a bit with what feasibly is there at times, but whatever level variety).