Over at the Hardball Times, Justin Inaz put together an excellent piece on the run scoring environments throughout the various minor leagues. If you pay attention to minor league ball, you know that the Pacific Coast League is notorious for being a "hitter's league", while the Florida State League is a much tougher run scoring environment. Thanks to Justin's work, we now have a snapshot of what the differences were in aggregate from 2007 to 2009.
The Yankees have teams in the Florida State League (High A Tampa), Gulf Coast (Rookie - also Tampa), International (AAA Scranton) and NY-PA (Short Season Staten Island) Leagues, which are the four lowest scoring leagues in the minors. They also have teams in the Eastern (AA Trenton) and South Atlantic (Low A Charleston) which are in the lower half of the bunch as well.
This means that Yankee pitching prospects who put up excellent numbers generally aren't quite as impressive as a hitting prospect who is doing the equivalent on the other side of the ball. And also that a pitcher in the Pacific Coast League with the same numbers as a Yankee farmhand in Scranton is likely to be pitching a whole lot better.
The difference between the Gulf Coast and Pioneer Leagues, which are both Rookie circuits is over 1.2 runs per game. Part of the reason is location. While the Gulf Coast League plays its games at or near sea level in humid conditions, the Pioneer League calls cities like Casper, Wyoming; Helena, Montana; and Idaho Falls, Idaho home, each of which is situated in the arid Northern Rockies at over 3,500 feet of elevation.
Of course, the size of the ballpark is also a major factor. Many clubs try to match their Big League parks to their minor league ones. This helps teams determine what kind of talent they have both offensively and defensive in the minors and eases the transition a bit when they finally call up their prospects.
The article at the Hardball Times also has a more detailed chart that includes the slash stats, home run rates and other pieces of data from the different leagues along with an explanation of the right column in the chart above - Base Runs. Check it out.