Try this link for baseball schedules

http://japanesebaseball.com/teams/index.jsp

If you're staying downtown, the two easiest teams to see are the Yomiuri Giants and Yakult Swallows since both are accessible on the subway. The Giants play home games at a covered stadium and seats are harder to get. The Swallows play outdoors and seats are usually available on game days. Night games are the norm in both cases. September weather should be OK for an outdoor game. For the best "experience" buy the cheap seats in the outfield since that's where the organized cheering groups are.