I skimmed the source code (base.js, light.js) to see what he was using. It appears to be entirely custom, with no graphics libraries like Three.js. He even implements his own low-level math functions from scratch. It's impressive to see that kind of discipline.
Honestly, if you’re wanting to produce something as good as this, Three.js or other such things just aren’t particularly helpful. It is easier to just ignore all the libraries and do it all from scratch. Popular libraries are good at producing finished products in a particular shape. When you’re wanting to demonstrate the implementation steps and allow intricate fiddling and have everything polished like you want it, they’re generally somewhere between painful and hopeless.
You could still keep Three.js for bits like vector calculations, but it just doesn’t feel worth it, it’s easy enough to implement yourself—or copy and paste from some such library and modify as needed—and will be much lighter. And you build up the bits and pieces you need over time.
What are some good sources to learn this kind of graphics programming work?
The best programmers are cautious about dependencies. Taking something is easy. But you don't learn. And you give up control.