。
Baseball is by far the most popular sport in Japan.
Literal
Baseball [topic-は] Japan [in-で] by-a-wide-margin number-one popular sport [copula-です].
とびぬけて ('by a wide margin, far and away') is the adverbial te-form of 突き抜ける ('break through, stand out'). Combined with いちばん ('the most, number one') it intensifies the superlative. 人気のある ('popular,' lit. 'having popularity') is the adjectival form of the noun 人気. A natural sports commentary sentence.