"Which one is the best" is obviously a question format, so it makes sense that " which one the best is " should be the correct form. This is very good instinct, and you could even argue that the grammar is good, but at best it's unnatural. Some people say a dog=one, dogs=ones, the dog=the one=that, and the dogs=the ones=those.

Understanding the Context

It's a rule of thumb, but what I found was that this is not always correct.