Managing a baseball team is not an easy job. The way I see it, one needs to have two completely separate, difficult to master skill sets, which may be why there aren't many great managers out there.
The first of course is game coaching. When to call hit and run, when to take pitchers out, etc. In and of itself, this is hard because it encompasses so many different skills (knowing when to bunt is entirely independent from knowing how to work a bullpen). There are a lot of variables in baseball, lots to keep track of.
The other fundamental skill is managing the personalities. This is tricky. I think the reason that so many managers are crummy in one situation and then good two years later with a different team is that they can run a certain kind of clubhouse, but not others. (All together now, repeat after me: "Buck Showalter".) As a sidenote, I'm not convinced that this is any harder today than it was 50 years ago. I'm convinced that major leaguers have always been a quirky, cocky, arrogent, talented, strong, macho bunch of jerks, generally speaking. (I'm reading an account of the 1949 American League pennant race now, and Ted Williams and Joe DiMaggio were as difficult as anyone today.)
I've been thinking about the job that Terry Francona did for the Sox this year. Obviously this was a team that could have exploded. Pedro is a deeply proud, tightly wound but somewhat selfish man, Lowe is an absolute head case, Manny Ramirez is, uh, Manny Ramirez, Curt Schilling is your basic jerk, plus you have your Johnny Damon sideshow, etc. etc. Plus there's the Globe and the Herald howling at any miscue. Francona was fantastic at getting all the pistons to fire together in this complicated engine. This was all invisible. He did all of his best work out of the public eye, which is of course by design. The frustrating thing was that his actual game managing was, shall we say, debatable. So we all saw the odd decisions and did not see the marvelous work that happened when there was no game going on.
Another manager cut from this cloth is Dusty Baker. Year after year he would coax career years out of retreads. Every year he would get fed a bunch of old players, including someone who you always thought "THAT guy is still in the bigs?" Every year they would become great hitters. And one must be impressed with anyone who can manage a team where Barry Bonds is *not* the biggest ass (Jeff Kent, come on down!). On the downside, of course, Baker never met a young pitcher who he wouldn't overwork. If I were the Cubbies, I'd be very worried.
In terms of the best managers, I think LaRussa is very good at both parts of the job. But one sometimes gets the feeling that he's more interested in being the Smartest Manager In Baseball than he is at winning games.
I think the best two are Felipe Alou and Joe Torre. You don't read about them doing a lot of yelling and screaming. They don't need to. They run their clubhouses and there's no doubt who's in charge. They also make good in game decisions. They're not perfect, but I think they're about as good as you're going to find in the game today.