Bartosz does an amazing job of making custom interactives and animations to support his articles. It looks like he uses custom canvas with webgl for the 3d renders.
There are 3d engines in JavaScript like three.js (https://threejs.org/) that can abstract some of the 3d rendering work for you.
I agree with naet that threejs might be the thing to look at if you want to make 3d animations. My own interactive diagrams are 2d, and I often use svg with reactive data filling in the parameters. [1] I've also tried hand crafting and it's not so bad for pages like this. They're mostly write-once pages, not software that's being maintained for many years. Some of our intuitions are out of whack when they tell us that we need abstractions and frameworks for maintainability.
What tool/library would you pick to create similar ones yourself?
Looking at the source [1], the author seems to hand-craft them using the canvas API, but man, that seems really difficult!
[1] https://ciechanow.ski/js/watch.js