I am using the D3 tree layout, such as this one: http://mbostock.github.com/d3/talk/20111018/tree.html
I have modified it for my needs and am running into an issue.
As of 2016, I was able to achieve this using just
tree.nodeSize([height, width])
https://github.com/mbostock/d3/wiki/Tree-Layout#nodeSize
The API Reference is a bit poor, but is works pretty straight forward. Be sure to use it after tree.size([height, width])
or else you will be overriding your values again.
For more reference: D3 Tree Layout Separation Between Nodes using NodeSize