I've found that a 10" tablet (a Touchpad in my case, though I imagine the experience with an iPad is equivalent) it pretty tough to beat for reference material. Doesn't have the navigation issues that the eink readers do, but it also allows me to make searchable annotations and highlights as I read.
Kindle is great for cover-to-cover reading, but for reference I will always prefer dead-tree (but will settle for searchable pdfs)