I use the Kindle app, mainly because it has a larger book selection and it is multi platform. That I own a Kindle may have also factored into my decision.
My main concern with Apple's ebook store is, that any books bought on iBooks can only be opened on Apple devices, whereas Kindle ebooks can be read on pretty much all modern devices.
For digital content, I don't see, why I should restrict myself more then necessary. Ebooks should be independent of the hardware, but iBooks forces you to keep using Apple hardware, if you want to keep access to the files. Hardcover books, paper backs can last decades, ebooks should last even longer. But who knows how the market will look like in 10-15 years. Steve will be gone and their products may not be the best on the market anymore.
My decision was simple, choose the one, which supports most devices, so that I can choose the hardware freely and then read the ebooks on it, it shouldn't be the other way around.
I know that I haven't addressed any of the actual features of the ebook readers, as consider them of secondary importance. But both are good for reading.
Btw. Barnes&Nobles is bankrupt, don't get their app, it has no future.