The wiki(baseball) seems like a good choice for this:
“Which team occupies the dugout on the first-base side or the third-base side is purely arbitrary. The Major League Baseball Rulebook is silent on the subject. There are many anecdotal reasons why one dugout is chosen over the other.[citation needed] One is that in the early days of the game the manager also served as the third base coach, so occupying the third base dugout meant less walking for the manager between innings. Contrarily, the thought is that since more close plays occur at first base than third, the first base dugout is preferred. However, the most likely theory is simply that the home team chooses the better clubhouse and the dugout on that side of the field. (For example, prior to their 2008 move to Nationals Park, the Washington Nationals occupied the third-base dugout at RFK Stadium because it was the larger and newer of the two dugouts.[citation needed])”