There's so many different opinions on this depending on who you ask. Numbers vary depending on what league and what era someone played in, so they don't tell the whole story. You have to consider how pure the era was in terms of drug use/steroids and what exact ball was used. Then you have to consider the idea that the National League may be a little more hitter friendly. Some people will look at the all-time stat leaders and come up with their own theories. Barry Bonds could have been one of the greatest but the fact that he did steroids will, IMHO, prevent him from every being seen as such.
I don't know who the best player ever was, but Babe Ruth will always be mentioned as a very likely choice.