If we are to use as little fan fiction/assumptions/w/etf you want to call it as possible, then the Minish only came to Hyrule twice. That means that TMC and it's backstory must come before OoT. I am just making as few assumptions and leaps of faith as possible. According to that, TMC must come before OoT (just according to that, though, as there is contradicting evidence that suggest TMC is post-OoT).