If you choose NY - call and see if you can get tickets for the stadium tour...
Personally, I've neen to NYC twice and I wouldn't go back....my next city trip will be to Washington....that said, your trip seems to be all about the baseball...Yankee Stadium is pretty sweet, but isn't the atmosphere s*** now as fans aren't filling it because Jeter is gone and they don't know the players names anymore? Last year there were only Jays fans in the seats after the 7th inning...