I'll second the Ban Johnson League as a great place for summer baseball.
http://bjbaseball.com/
Will Rogers coaches the KC Blues and is lots of fun. This would be my son's first choice to play just because Will puts so much into it. He's a great guy.
UMB Bank, BJ Raiders and the Royals are usually the top teams.
The All-star game is played at Kauffman stadium. Pretty cool to play on an MLB field.
There's also the MINK league, but more travel is involved.
http://www.minkleaguebaseball.com/
Good luck!