There are a couple ways of doing baked shadows that you can use with three.js:
An AO map can be embedded in the model in formats like glTF (see https://github.com/KhronosGroup/glTF-Blender-IO), which three.js can load via
THREE.GLTFLoader. I'm not aware of a way to export the lightmap as part of your model, so you'd probably need to load it separately via
In either case, the material can be modified independently of the AO or lightmap.
Finally, you could also bake the shadows directly into a base color texture, but then you lose the option of modifying the material in three.js.