Wins Above Replacement seems to be a growing favorite when comparing dominate players of one era from another:
http://www.baseball-reference.com/leaders/WAR_career.shtml
However, there are some factors which are not included...and ones I cannot ignore.
I've long thought that the best ball player before the 1950s never played Major League Baseball. Josh Gibson is a very good possibility. And though the likes of Cobb and Ruth were great, they did not play against "the entire field". They only played against white players. That knocks all of them (including Gibson, since he mainly played only against black players) out of the running. Unfortunately, this also knocks out a couple of dominate players in Ted Williams and Stan Musial. Granted, they played a lot of years after the color barrier was finally broken...but many of their prime years were before blacks were finally allowed on the field. With a lot of regret, they go out.
The likes of A-Rod, Bonds and Clemens rate rather high...but let us face it, their records are quite tainted. Granted, if we look at the records of all three even before their suspected steroid periods, they were quite dominate...but there are too many question marks. Off they go.
That still leaves some rather good players. Mays. Aaron, Mantle. Rickey Henderson is surprisingly high. Schmidt. Frank Robinson. Tom Seaver is the highest ranking pitcher of those who made my cuts. Joe Morgan. Eddie Matthews. Greg Maddox. Niekro, Bob Gibson and Gaylor Perry round out our pitching staff (Niekro and Perry and surprising picks, until we realize that they won a lot with some really bad teams. BTW, if we skip down two pitching spots - past Randy Johnson and Spahn, Blyleven would have made the list. And it took so long for him to make the Hall why?). The highest ranked shortstop would be Cal Ripken Jr. Johnny Bench is our highest ranked catcher.
For the curious, the top active players in order are A-Rod, Pujols, Thome, Jeter and I-Rod.
As a gut reaction, I would have chosen Ken Griffey Jr., as well. He is ranked a lot lower than I would have expected, 60th all time, but still as low as 30th after I make my cuts. The injuries while he played with Cincinnati took their toll. New Hall of Famer Barry Larkin ranks 90th.