If you are writing a normal book and you're already familiar with Leanpub-Flavored Markdown, it is probably the better choice for now, because you don't have to learn anything new, and you can just get to writing your book :)

 However, Markua will eventually be a lot more robust for writing books than Leanpub-Flavored Markdown. It has not been fully implemented yet, but you can read about it here: https://leanpub.com/markua/read.

In addition to creating books, you can also use Markua to produce MOOCs from plain text documents; you can't do this using Leanpub-Flavored Markdown.