Keep in mind that when BA says that Latimore is the Pirates' best minor league power hitter, it isn't necessarily saying that Latimore's a great prospect, only that in terms of tools, he's the best at hitting for power. BA has Justin Bencsko rated as the Pirates' fastest baserunner, but I seriously doubt anyone at BA thinks Bencsko is a great prospect.
Completely abstracted from any other consideration, Latimore has excellent power. He had 52 extra-base hits this year, 19 of them homers, which is excellent for a 21-year-old in Class A+. He also had 45 extra-base hits the previous year. Where Latimore gets in trouble is with his strike zone judgment. He has posted about four strikeouts for every walk in each of the past two years, which doesn't bode well, because while he clearly can hit for power, major league pitchers will easily be able to neutralize that skill unless he improves.
Brad Eldred (who BA rated as the top power hitter in the Pirates' minors in 2005) had an incredible ability to hit for power, but he couldn't do much with it because it was his only tool. It's too early to say that Latimore is as one-dimensional as Eldred was, but it's certainly a concern. That doesn't mean that BA got it wrong, in either case.
So: if Latimore isn't the best power hitter in the Pirates' system, in terms of tools, then who is? You could certainly make cases for several members of last year's West Virginia Power team. Jarek Cunningham clearly has terrific power - the ball jumps off his bat, and he had 56 extra-base hits last year as a 20-year-old. Evan Chambers, Rogelios Noris and Aaron Baker are also possibilities. Purely on tools, Jesus Brito has good power too, although that's about the only thing he has.
Andrew Lambo, who hit 39 doubles as a 20-year-old in Class AA in 2009, is another possibility. And if you want to get speculative, you could pick Jared Lakind, who's all the way down in rookie ball, or maybe Matt Curry. All things considered, though, Latimore is who I would have picked as well.