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!
You can access Jingu Stadium via subway or train. If you're coming on the subway, there are two options: Tokyo Metro Ginza Line(G03) Gaiemmae Station (5 minute walk from Exit 3) or Toei Subway Oedo Line(E25) Kokuritsu-Kyogijo Station (12 minute walk from Exit A2). You can also take the train and get off at JR Shinanomachi or JR Sendagaya stations (15 minute walk from either station exit).