First, iPads are not eBook readers. Their screen is more along the line of an active screen that can display well. Of course, this will be harder on the eyes for long term use than a Nook or a Kindle which uses eInk which is easier to read, but does not have the fast refresh rate of a LCD.
If I were deciding:
If I wanted a general tablet device, I'd go for an iPad, and jailbreak it.
If I wanted an ebook reader, If I wasn't needing the Kindle per se, I'd buy the Nook. Reason? It runs Android, so it can be rooted and customized to do cool stuff.