I have been trying to export a skeletal animation, from Maya 2013 to THREE.js for quite some time, and I haven't seen this exact issue come up yet...
After getting frustrated for it not working. I resorted to copy and pasting the monster example then placing it with my model, my model has lost its animations. :( I baked them and everything when I exported in FBX-DAE.
I do get a warning but i don't know if it matters: could not find transform "visibility" in node joint1.
Have you tried the OpenCOLLADA exporter?
There's a new project under way that might be of interest to you. Export path would be Maya > OpenCOLLADA > gltF > Three.js
Here's the glTF loader for Three.js: https://github.com/KhronosGroup/glTF/tree/master/loaders/threejs