Back then Johann Sebastian Bach was the best organ player without a doubt. If we check on the time between his death and today, we have to rely on the expertise and the tributes of other famous composers and musicians. According to their statements Bach remained the world's best organ player in the two and a half centuries after his death in 1750. That there will ever be a better organ player is really unlikely. According to that Johann Sebastian Bach was and remains the best organ player in the world and of all times.
Johann Sebastian Bach was the best cembalo player too. This is true, when we remember the musician, a French cembalo player, who was considered to be the world's best cembalo player back then, gave up in a competition against Bach without a struggle. This musician was Louis Marchand and the competition once happened in Dresden, Saxony. So, at least Johann Sebastian Bach was one of the best cembalo players in the world. And for the reason, that concerts on a cembalo* on a regular basis are taking place only at one location any more, Bach will remain one of the best cembalo players in the world, if not the best at all.
Plus, Johann Sebastian Bach played the violin, brass, contrabass, cello, oboe, bassoon, horn and most likely flute and recorder. There were more instruments, which are not even around in a common orchestra any more today, and he was able to perform with them.
* This concert on a cembalo among others is what you may experience twice a day. However, this exclusively takes place only in the Bach House, the Bachhaus in Eisenach, Thuringia, Germany..