There is only one team in MLB that has a winning record against every division and Interleague. That teams is the Philadelphia Phillies. The Fightins are 18-12 vs. the NL East, 5-3 vs. the Central, 9-7 vs. the West (no thanks to Brad Lidge) and 2-1 vs. the AL.
Los Angeles has the MLB's best record at 40-21, but it appears to be largely the result of playing in the NL West. The Dodgers are 26-10 in their division; 14-11 elsewhere. Consider, the NL's worst teams outside of the West -- Florida, Washington, Pittsburgh and Houston -- are a combined 25-19 vs. the NL West.
If the Phils can ever figure out how to win at home (12-14) they might be the best team in baseball.