Hrm. I think to a certain extent, that's like "who's stronger, Clark or J'onn;" once you're at the point where you're pulling planets out of orbit, arm-wrestling contests become relatively meaningless. Once you're thinking rings around the opposition on Diana and Bruce's level, who wins at go is similarly empty (offhand, they'd probably trade victories at a nearly 1:1 ratio, and always by narrow margins).
But I'd tend to agree with arrlaari that Bruce is better at strategy, and Diana (and Oracle, incidentally) is better at tactics; drop both of them into a battlefield out of the blue, she has a much wider and more instinctive arsenal of tools and can respond much better to the changing situation than him, but give them a few days to prepare, and he'll come up with a way to completely circumvent most of the battle that she wouldn't have thought of. Not that they're not both quite competent at both, but he's a marginally more optimal coach than she is, and she's the marginally more optimal captain (and wow, how much do I want to see the League play hockey suddenly?).
Where Diana gets the edge is that she's a better leader than him; Bruce can make effective, loyal soldiers out of certain very special people whose weirdnesses line up with his and who are constitutionally suited to tolerate his bullshit, while Diana can make effective, loyal soldiers out of pretty much anything that breathes, and also robots. All Bruce cares is that people do what he says, right now, and if they sulk and quit later, well, that's trimming the fat; give him six people, he can win the battle and save the world, and he's done his part. Diana cares that people are satisfied and on-board and feel connected, and if they aren't happy, she'll do her damnedest to change that; give her six people, she'll make a League out of them, win the battle, save the world and have them all saving the world tomorrow, too, and their own lives will be better for having been a part of it. This only exacerbates the divide between their methods, since it means she's more likely to have more resources available when she's being reactive, and he has a greater need to create long-term plans that ensure the resources he has will be sufficient.