I agree with Vee41 regarding the webGL effect being the simplest solution. However, this option will only work on webGL enabled devices. Also, you'll need to use a separate sprite for each body part you want colored, and layer them appropriately during runtime.
Here's an example:
If it were my game, I'd probably create a few canned color options that are hard coded instead of having to worry about color layers, and webGL enabled devices.
I hope this helps.