IMNSHO, the best e-book app is the one that'll read the e-book you've bought. Most of the readers are produced by companies that put DRM on the e-books to "protect" them (I think it's mostly to lock you in to their reader ... and so buy more books from them ... but I digress). This includes Amazon/Kindle.
So, you can't buy a Kindle book from Amazon and try to read it on iBooks, and vice versa.
My suggestion for the best reading app (since the app itself is free) is to buy your e-books from the cheapest place and then use the free app to read it. Well, that's what I do. YMMV.
For non-DRM protected books ... I don't have a preference (though I do find myself using Stanza a lot...).
Happy reading!
Marilyn