What constitutes the best pitcher season in the sim might be a matter of debate. If we do it based on WAR, then Hal Newhouser takes the cake. His 17.7 WAR translated to a 30-11 record with a 1.69 during 1945, including 308 strikeouts at a time that was truly remarkable, as was his 373-1/3 innings pitched. His ERA+ that year was 230.
If you're more a fan of the straight ERA approach, Rube Waddell's 1908 is for you. He had a record 1.10 that year with an astounding 35-4 record. His ERA+ was 236, which is a little better than Prince Hal's 1945.