It is a sad comment on our society (read: US) that this question can actually exist. It is a shame that racism was so prevalent in the first half of the 20th century that blacks (or African-Americans if you prefer, or Negroes, as they were called back then, hence, the name of the leagues) were not allowed to play in MLB. White players refused to play against blacks and, judging from the fans' treatment of Jackie Robinson (as you know, the first black to play in baseball  since the late 1800s) at first, many of the fans did not want to see blacks in baseball.
At this site, I put a disclaimer under the baseball category encouraging voters to consider the players from the Negro Leagues. Unfortunately, it is just a guess where to rank the players from the Negro Leagues for several reasons. First, many of them never played in the majors, or when they did, they were past their prime.
For instance, the legendary Satchel Paige did not start pitching in the majors until he was around the age 42 or 43 (depending on which date of birth you believe).
Second, the statistics from the Negro Leagues were incomplete.
Third, those statistics are almost meaningless when comparing them to the MLB statistics, since the quality of the Negro Leagues were hard to determine.
Fourth, the leagues were different statistically: From 1930-1950, the batting average in the Negro Leagues was .308, while the batting average in MLB was .269. This difference was apparently (from what I read, including quotes from Negro League hitting stars such as Buck O'Neil) the result of a lack of pitching depth in the Negro Leagues. A study of 15 Negro League stars (including Roy Campanella and Willie Mays) that I saw showed the same players hitting .319 in the Negro Leagues and then .271 in MLB.
You may have heard claims that the Negro Leagues were actually stronger than the majors because they consistently beat them in exhibitions. Well, yes and no. Competing Major League teams rarely had all their players from big league clubs—many of the players that played in these exhibitions were minor league players.
Here is a study I found on the Internet from a blog on baseball-fever.com. The numbers on the right; e.g. 4-6, were the number of MLB players that played in the games; "Major League Team" means that most of the same players were from the same team played (games included are between 1902-1946):
Negro League Teams vs. Major League “All-Stars” (0-3)
Negro League Teams vs. Major League “All-Stars” (4-6)
Negro League Teams vs. Major League “All-Stars” (7+)
Negro League Teams vs. Major League Team (4-6)
Negro League Teams vs. Major League Team (7+)
Negro League vs. Major Leaguers (4-6)
Negro League vs. Major Leaguers (7+)
I will let you draw your own conclusion from all of this. However, I will say that while the MLB might have had more depth than the Negro Leagues, it seems obvious that the stars in the Negro Leagues would have been stars in MLB.
Joe DiMaggio called Paige the best pitcher he ever faced (you would think he would know). Was Satchel the best pitcher ever? Was Josh Gibson the best home run hitter ever? Was James "Cool Papa" Bell (great nickname) the fastest player and the best base stealer to ever play baseball? How great an all-around hitter was Buck Leonard?
I do not have a definitive answer to any of these questions and, sadly, neither does anyone else.