Here's a list of the top 5 batting average seasons for Brewer minor leaguers over the last 10 years (min 350 PA):

*0.360 - Angel Salome (Huntsville 2008)
0.354 - Jim Rushford (0.363 in 259 AB in High Desert / 0.342 in 187 AB in Huntsville - 2001)
0.345 - Andrew Lefave (West Virginia 2007)
0.336 - Bobby Darula (0.384 in 237 AB in Beloit / 0.239 in 117 AB in Huntsville - 2000)
0.335 - Eric Fryer (West Virginia 2008)

*Salome went 0-3 for Milwaukee that season.

A little more about the leader, Angel Salome

(photo from the Yahoo!)

Drafted:                                   Drafted in the 5th Round in 2004
How Acquired:                       Drafted by Brewers
Years with Brewers:              5
Best Season:                         2008 - Hit .360/.451/.559 for Huntsville with 83 RBI. 
Last Professional Season:  Played in Nashville in 2009 hitting .286/.334/.413
Other Notes of Interset:        Salome was drafted two picks ahead of Paul Janish, the immortal pitcher/shortstop for the Reds.

For more interesting tidbits on Salome, see this post from 2007.

Ranked #5 prospect in the Brewers system by Baseball America after the 2008 season.
Ranked #8 prospect in the Brewers system by Baseball America after the 2007 season.
Noted as the "Best Defensive Catcher" in the Brewers system by Baseball America after the 2004 season.

2009 Leaders (min 350 PA)

0.316 - Jason Bourgeois (Nashville)
0.311 - Hernan Iribarren (Nashville)
0.308 - Logan Schafer (0.313 in 457 AB for Brevard County / 0.217 in 23 AB for Huntsville)

Honorable Mention: 0.345 by Sean Halton in just under 300 PA between Helena and Arizona