Look into http://www.highcharts.com. Much more high level than D3, does nice charts and graphs. Free for non-commercial, and reasonably cheap for commercial work.

The other really useful tool is Tableau Public, if your data isn't confidential. GUI interface, but makes visualizing information really easy.

The other tool I use a lot is http://p5js.org. It's more a general-purpose drawing tool, but if all you want to do is put some boxes at (x,y) positions, it's a really good prototyping tool.