The speed and responsiveness of Canvas for complex visualisation (ones where there are a lot of objects) means it's often the better choice. However, libraries like d3 make working with SVG a lot easier.
I'm interested, why does SVG seem to de the default choice for web graphics? And is there something like d3 that makes working with Canvas more accessible?
D3 Version 4 has more utilities and examples of interactions with Canvas. Here's an example of a relatively small graph (~500 nodes, 10k edges) that SVG used to struggle with, but Canvas renders with ease.
http://bl.ocks.org/syntagmatic/954b31aa8b8beb91b30ccb0c9e57f...
Notice the nodes are draggable, an interaction supported by the new simulation.find https://github.com/d3/d3-force/#simulation_find