Gwynn and Boggs, pictured at the 1987 All-Star Game in Oakland (SI Photos)
Both debuted in 1982, won multiple batting titles, and joined the 3,000 hit club in 1999. They were perennial All-Stars, multi-Gold Glove winners, and first-ballot Hall of Famers. They played 2,440 games apiece--all with the same team for one, all in the same division for the other.
I don't mean as players, because WAR makes it pretty clear that Boggs was better (he has a 20-ish edge in bWAR, fWAR, and WARP). I mean as hitters, because they're career numbers are so darn close:
Boggs 1,513 R 3,010 H 578 2B 118 HR 1,014 RBI .328/.415/.443 (132 wRC+) 1,412 BB 745 K
Gwynn 1,383 R 3,141 H 543 2B 135 HR 1,138 RBI .338/.388/.459 (132 wRC+) 790 BB 434 K
As you can see, it's a virtual wash. Boggs scored more runs, but Gwynn knocked in more. Boggs stroked a few more doubles, while Gwynn socked a few more homers. Boggs walked twice as often, but also struck out twice as much. Boggs got on base more, but Gwynn had more hits and greater power.
I was hoping advanced metrics might reveal a significant difference, but once again it's really close:
Boggs: .302 tAVG .381 wOBA 1,750 RC 479.7 BtRuns
Gwynn: .300 tAVG .370 wOBA 1,636 RC 437.7 BtRuns
Boggs comes out on top, barely. His edge in adjusted batting runs is roughly two per season, while his advantage in runs created is about four per year. You're splitting hairs at that point, albeit in Boggs's favor.
But then, Boggs spent much of his playing days in hitter's parks--nobody took greater advantage of Fenway--whereas Gwynn spent his entire career in Qualcomm Stadium--the Petco Park of its time. Accordingly, when you neutralize their numbers, Gwynn's get better while Boggs's get worse:
Boggs .321/.407/.435 (.842 OPS) 1,664 RC
Gwynn .340/.391/.461 (.852 OPS) 1,735 RC
Now it's flipped, as ir's Gwynn who holds the slight edge. I think if you put him in Fenway Park, he probably hits .350 for his career. Meanwhile, had Boggs spent his whole career in San Diego, he wouldn't have come close to batting .328.
Boggs could hit anywhere--he batted .302/.387/.395 on the road--but that would have been a bad season for him. It also pales in comparison to what he did at home (.354/.443/.495). Most hitters benefit from their home parks, but not to the same degree that Boggs did (unless they play in Coors Field).
Gwynn, on the other hand, hit nearly as well on the road as he did at home. His .334/.384/.451 road averages are nearly identical to his .343/.393/.466 home record. Gwynn would have been a .330 hitter no matter which team he played for, but Boggs might have batted closer to .300.
I went into this post thinking Boggs was the better hitter due to his gaudier on-base percentages and almost-even power, but after taking their environments into account it appears Gwynn was the superior batsman.