fourdimensions.js is a tool for visualising 4-polytopes. It is extensible (although a bit of a pain to extend) and uses three.js as a display library. My main references in creating fourdimensions.js were Four-Space Visualization of 4D Objects by Steven Hollasch and this site on interpreting projections from 4 dimensions. You can see the script in action here.
##License fourdimensions.js is under the MIT License if you want to do whatever with it.