The word "best" is an adjective, and adjectives do not take articles by themselves. Because the noun car is modified by the superlative adjective best, and because this makes the noun car definite in this context, we use the. It is best not to do something. Here, we have the adjective best, but this adjective is attached to no noun.
"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's best that he bought it yesterday. or It's good that he bought it yesterday. 2a has a quite different meaning, implying that what is being approved of is not that the purchase be made, but that he is the one to make it.