Hmmm. It seems that the same book is sold on both stores. Why are there two different stores? They appear to be identical. IMHO, either the different stores should recognize the book as the same object or the App Store should quit selling books. Just a rough edge on an otherwise great product.
In many cases books sold in the App Store are enhanced in ways ePubs can not be, though ePubs have gotten more bells and whistles lately. For children's and interactive books, the App Store is the only way to publish. There is a recent Kennedy memoir book (can't remember the name) that is packed with video and other features.
The iBook store is more recent, and sells the more traditional notion of a book. Recent additions to the ePub format have made it possible to add audio, video, and force a layout, so you may see more multimedia books showing up there, but for real interaction, you'll still need to create the book as an app.
Finally, and sadly, there are a glut of App Store books that offer nothing a standard eBook can't. I avoid these because they take up too much space for what you get.
When deciding between an App Store book and iBooks (or Kindle, or etc) read the App Store description closely and see what more you'll be getting, and decide if it is worth it.