WebGL:

☛ WebGL allows you to control the GPU in more direct way

☛ It is more an “immediate mode”

☛ It does not have additional support for text, for shaders built, for picking, etc.

Three.js:

☛ Three.js is built on top of WebGL and allows you to take care of lot of things like what objects to draw each frame

☛ It is more a “retained mode”

☛ It does have an additional support for text, for picking, for object hierarchy, etc.