I think you're on the right track with looking at WebGL, but depending on what you're doing in your visualization you might need to get closer to the metal than "out of the box" threejs.
I recommend taking a look at GLSL and taking a look at how you can implement your visualization using vertex and fragment shaders. You can still use threejs for a lot of the WebGL plumbing.
The reason you'll probably need to get directly into GLSL shader work is because you want to take most of the poly manipulation logic out of javascript, at least as much as is possible. Any time you ask js to do a tight loop over tens of thousands of polys to update position, etc... you are going to struggle with CPU usage.
It is going to be much more performant to have js pass in data parameters to your shaders and let the vertex manipulation happen there.
Take a look here: http://www.html5rocks.com/en/tutorials/webgl/shaders/ for a nice shader tutorial.