There's lot to be said for using multiple ebook readers. I use the Kindle app, Books, and ShuBooks — two different versions of it.
The Kindle app is great for the free Prime Reads we accumulated over the years and for direct access, including browsing and searching, to the marvelous New Oxford America Dictionary that's included on all Macs and i-devices. ShuBooks is a fantastic ebook reader with full-fledged controls — think Stanza — and a much better interface for book collections than Books. Having multiple ebook apps per its one to read different documents and books and switch between them by simply opening the other app. Navigating around Books is a mess. The lack of color controls is frustrating, too.
As to synching, ShuBooks works well through iTunes, an easy matter of drag and drop to upload or download. Kindle synchs well, too. Apple's any Ching is a mess if you've accumulated different books on different devices. Last I checked this, you were forced to accept a clearing out off ALL the ebooks off of your device. Very bad form. ShuBooks and Kindle merge books seamlessly.
So, for the OP, you don't necessarily need to make this an either-or conundrum. Use both Kindle and Books — and check out ShuBooks, too!