iBooks is my app of choice. It does what I need and is not too bad at syncing between my devices, which is not easy since I mostly read on the train where I can't get 3G. Many apps have difficulties syncing when the device is not online all the time, but Apple apps manage this better than most.
In some cases when I buy a book and am unable or unwilling to convert it, I will read it on the seller's app, usually Kindle and recently (once) Kobo. The Kindle app is OK but I prefer to buy ePub books when I can. The Kobo app is the worst. Can you imagine a reading app without a search function? Well, Kobo can apparently. It has Facebook but no search.