It's not the biggest or most modern baseball stadium in Tokyo, but Meiji Jingu Stadium in Shinjuku is worth visiting for it's unique atmosphere and history. Opened in 1926, it's one of the few stadiums still in existence where Babe Ruth played (along with Lou Gehrig on a 1934, 22-game tour of Japan).
Today it's home to the Tokyo Yakult Swallows, as well as a popular host of many college match-ups. If you have time, it's an excellent place to watch a game. Because it is rather small nearly every seat is close to the field. Unlike in the US, Japanese baseball is a very rowdy interactive game for fans with organized chants, dancing and cheerleaders. The traditional way fans cheer for the Swallows is to open their umbrellas and sing a song, so be sure to come prepared!