From someone who likes to look at these kinds of libraries... D3.js vs animation/graphics libraries: D3.js targets processes over arrays of data, perfect for designing views of data; these other libraries (like raphael.js, jquery.svg, etc) target transformations and tweening, perfect for objects in motion.

This compares better to Raphael. D3 is a library to present data visually, and Bonsai is a drawing library.

You can draw with D3 and you can produce data visualizations with Bonsai, but they each shine in their own area. Creating a simple bar chart with Bonsai wouldn't be easy, the same thing goes for drawing a star in D3.