"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.
It is possible that the singular/plural choice is not a purely syntactical matter, but partially depends on whether the speaker's focus is on one or on more. If it is expected that there will be more than one (and one is included just to cover all the possibilities), it is natural to use the plural.