The Gambo/Spritze database contains Negro League players, but I don't think it would help you with actually creating any league structures or setting up your baseball universe.
Also, the database contains a lot of career minor leaguers, Japanese league players from past eras, and possibly some other prominent players that never made it to MLB.
And their file is just a database. It wouldn't provide logos and uniforms, but you should be able to download those from the appropriate sections on
OOTPMods.com. Then again, those are for Facegens, and I don't think there is a historical Negro League Facegen pack or anything like that. So the uniforms are more for fictional leagues. But I think Negro League players may be in the big photo pack that is available on the site.