I think the main thing is deciding what features your book needs. If it's basically a text based book and all you care about is a page turning effect, you have a lot of options for reflow EPUBs. Pages now offers fixed or reflow options.
If your book needs to be feature rich with a lot of interactive elements, you're probably looking at a fixed layout EPUB or .iBooks multi-touch (no page turn most likely). Also, do you need to hit other platforms. If yes, check to see if they accept both EPUB 2 and 3.
There are plug-ins for InDesign from places like Aquafadas, and you can integrate HTML5 from apps like Hype.
If you just need simple EPUB, other options are Vellum, Scrivener, Calibre etc.