I've been thinking alot about this since I finished the game, and from what I've seen in the game, I believe this game is not down any of the currently known timelines. There are plenty of references to each of the timelines which contradict each other. Naturally this would make a timeline placement difficult, but to be honest if you think outside the box, an answer may be more clearer than you think.
I'm not gonna go into too much detail, but with the Zora Monuments mentioning Ruto and there being no mention of a great flood, it could be possible that BotW takes place on a 4th timeline where Link stays in the adult timeline after OoT and he or a decendent defeats ganon during the back story of Wind Waker, thus preventing the great flood from happening and in turn BotW happens. This would clear the contradictions to the Zora Monuments at least, but there are other factors to take into consideration.
Of coure this is just speculation and there is more to this theory, but for the purpose of this thread I'm gonna say there's no straight forward answer to this puzzle at the moment and won't become clear anytime soon until Nintendo or Eiji Aonuma comes out and says something.