This debate is as tight as any position in franchise history. It’s uncanny how similar they are at the plate and in the field, making any minor advantage one of them has in a particular area essentially a wash.
If we were picking the best individual season by a Red Sox second baseman then Pedroia is the clear winner. The 7.9 fWAR he produced in 2011 is the best single-season mark in franchise history at the position and his 6.4 fWAR from his MVP season in 2008 is next on the list.
The rest of the top 10 seasons for a Red Sox second baseman is mostly made up of Doerr, who topped out with a 6.0 fWAR season in 1942. For what it’s worth, Baseball-Reference values Doerr’s 6.3 WAR in 1944 as his best, although they are even higher on Pedroia’s best seasons.
Pedroia is the more decorated player with the higher peak but Doerr was more consistently productive over a longer period. Doerr already has a well-earned spot in the Hall of Fame while the injuries that have derailed the end of Pedroia’s career might keep him out of Cooperstown.
If you needed one Red Sox player to fill the position with their best season then it’s Pedroia, but as far as overall career, give me Doerr as the best second baseman in franchise history.