The best replacement for three.js is webgl.

The best alternatives to three.js are rated as following:
★★★★★  webgl
★★★★  famo.us
★★★  away3d
★★★  pixi.js
★★★  x3dom
★★  babylon.js
★★  d3.js
★★  processing.js
★  kineticjs
  philogl

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Speaking about three.js, one probably shouldn't forget about webgl.

Other search terms related to three.js and their ratings are:
★★★★★ webgl
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Google Trends

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three.js
webgl
famo.us