the Nook iPad app is much better than the nookcolor stock reader. The Android app might be as well, but my nookcolor isn't rooted so I don't know. Hopefully the promised upgrades we all expect to see in the coming weeks will greatly improve the non-rooted apps.
I've got both the nookcolor and an iPad 1 and I'm really leaning heavily toward the iPad. If I had to give up one right now, which I don't, I would give up the nookcolor, but that is mostly because I've been using an iPod touch for a couple of years or so and I'm therefore much more familiar with iOS than Android. I've tried to get to know Android through some other tablets and let me just say we have agreed to keep our distance from one another!

For me the bottomline is I can quickly and easily get done what I need to in iOS, but not so much in Android. Both OSes are really lacking IMHO when compared to MacOS or Windows.