Personally, whatever helps with the specific writing part of it all the most is what's best. If you find writing in a given dialect of Markdown or LaTeX or Org-mode is easiest, do that. For me, that's Markdown with embedded LaTeX, for others it's Org-mode, or RST, and so on.
Pandoc handles these fairly seamlessly, and with many options for PDF engines, though I'd say it has a preference for LaTeX and HTML in the backend and Markdown in the frontend, based on my experiences with the edge cases (sometimes entirely solvable with a little Haskell or Lua).
Since LaTeX is the default for PDFs, it pays to keep that in mind and help LaTeX help you (you can use it inline with Markdown or included as preamble in configuration), but sometimes I've just had better luck converting via HTML to PDF ("-t html output.pdf" or directly chaining on from output.html) for what I'm writing in the moment, though other times I'm not stressing LaTeX as much and can just go straight from Markdown to PDF (for example, just writing up something with inline maths). I prefer to avoid LaTeX or HTML's escaped character encoding and often need far more than a single Latin font can provide, so I've ended up dealing with LaTeX's limitations here (even in lualatex and xelatex) more than what I'd suspect is typical. Meanwhile, the standard HTML to PDF backend uses Qt, and I've found it works for everything else I've needed when LaTeX isn't the right backend (and it does come up). On one occasion, I did have to switch that to weasyprint, and that was everything sorted. Alternative backends is an unsung power that few have, while pandoc not only has many built-in (or it is at least internally aware of) but will also integrate with any CLI needed.
Output to all three with HTML, EPUB, and PDF can just need a bit of fiddling before it comes out right, depending on how much you're willing to mess with specific metadata for each versus accepting the limits of what Pandoc can handle universally in its AST. Invariably, some compromise is required, but the core semantics of Markdown (including extensions) almost always translate without an issue. The dialect problem of Markdown is really just in the confluence of said semantics with things that have not been separately included, such as the lack of an actual header in Markdown (Pandoc here allows YAML for some, or you just fall back to HTML).
So, tldr; there's no "best" input format, except the one that you find most comfortable to just write the book in, but I find Pandoc is usually best approached from Markdown with the LaTeX or HTML backends. It's powerful and oh so very handy, but it's not going to do all the thinking for you, just a lot of the grunt work, same as any other tool. When in doubt, the user manual is quite readable, and I've found it answered almost every question I had. When it doesn't, other people do, and when they don't, it means I'm either going about it the wrong way or I get to solve an actual problem (but usually the former). But, as always, the most important thing is actually writing it, distribution comes later, so focus your efforts on that and the tools you need to do that effectively.