Encyclopedia of Minor League Baseball, 3rd ed. by Lloyd Johnson and Miles Wolff (c) 2007 ISBN: 978-1-932391-17-6
Excellent for identifying what the leagues were for any given year, which teams were in which leagues, who the president of each league was for each year, etc.
Otherwise, as stated above, baseball-reference.com/minors/ is an excellent resource. They have been collaborating with SABR to fill in the information, and have made strides in recent years. As expected, the further back you go, the more spotty the roster info gets (often just last names on the rosters), but it's definitely getting there.
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