I'd say the Braves. Even though the Yankees won 3 championships in the 1990s, the Braves won 8 out of the possible 10 division titles (8 out of 9 if you don't want to count 1994) in the '90s. The Yankees weren't so good from 1990-1992 with W%s of .414, .438, and .469 respectively. Gotta be the Braves.

Cowboys