Unless you just want to use the Nook app, the iBooks app will work fine. The way I usually move books to the iPad is to attach them to an email and send them to myself. Or you can use dropbox. Then when you go to open the attachment it will give you options to use depending on what reading apps you have. I have the Nook app installed on my iPad, and 6 options for opening an ePub I sent myself, but I don't see the Nook app as one of those options. Not sure why.
em Kindling since August 2008, Kindle Fire, K$79; Nook Color w/N2A card; iPad1