The topic of who was the greatest pitcher, like the similar one of the greatest player of all-time is one that every serious baseball fan has engaged in at least once, if not several times. The long history of major league baseball as an integral part of the national consciousness, its continuity of rules since the late nineteenth century, and its plethora of statistics that help define individual performance makes it ripe for comparing legendary players across eras.
Interpreting the question as who had the greatest career for a starting pitcher, the factors should incorporate the total number of wins (that’s what starting pitchers are ultimately paid to do) and naturally the winning percentage. Plus, it should also include the ERA, but a much better way to do this is by factoring in how much lower the pitcher’s ERA was versus the league, as this helps level the greatly dissimilar eras. And, it should contain the difference between each pitcher’s winning percentage and his teams to mitigate the advantage of playing on good teams when also using the absolute winning percentage. The factors have the following weighting, reflecting my beliefs (and biases) after following baseball for nearly four decades:
30% - Winning % > Team Winning %
30% - ERA < League ERA
20% - Overall Winning %
20% - Total Wins
Using these factors the list in descending order would be: Cy Young, Walter Johnson, Roger Clemens (strictly by the numbers…), Christy Mathewson, Lefty Grove, Grover Alexander, Randy Johnson, Greg Maddux, Pedro Martinez, and Tom Seaver. Though his major league numbers don’t reflect it, a good case for Satchel Paige might be made for his inclusion among the very best ever. The table below provides data on the top twenty-five starting pitchers of all-time according to this calculation. I find it interesting that four of the top ten are pitchers who were active in 2007. It could be that the dilution of talent by increased teams and rosters, modern medical techniques and the salary incentive to stay active as long as possible are likely some of the most significant reasons for this.
Sandy Koufax and Nolan Ryan are two names that seemingly always come up when the discussion turns to the greatest pitcher ever. Sandy Koufax’s four seasons, which are probably the best four consecutive seasons ever, are not enough to qualify as having the best career. He is number 26 on the list. As for Nolan Ryan (number 30), I loved to watch him pitch in the Dome as kid (along with JR Richard), but he really does not deserve to be mentioned among the top couple of dozen starting pitchers of all time. True, he pitched on mediocre teams for much of his career, but his winning percentage was only slightly higher than his teams. Though his ERA was very good, it was not as much lower versus the league (15%) as the other top pitchers over the years (20% to 35% for the ten listed above). If not one of the very greatest starting pitchers, he was certainly the greatest strikeout pitcher of all time, though.

Table - Top 25 Starting Pitching Careers in Major League History
The leaders among the top starting pitchers of all-time in each category are highlighted in bold above: Cy Young for both wins and losses (511 and 316, respectively); Randy Johnson has the winning percentage that is the best in comparison to his teams; Pedro Martinez has the ERA that is lowest compared to his league averages; Whitey Ford has the highest winning percentage; and, Ed Walsh has the lowest ERA.
This might not be the definite answer to the question of who is the greatest pitcher in major league history, but there is some pretty good substance in the argument above.