As Coremiller notes, soccer is virtually impossible to compare across eras. Not only that, but comparing players from different positions is also basically impossible as well, you can't really compare Beckenbauer and Messi, just like how you really couldn't compare Jerry Rice and Tom Brady, or Walter Johnson and Ted Williams.
Soccer is a global game, and only until recently did certain leagues become big enough to really justify being truly international collections of talent. That means that for a majority of the game's existence, we had to basically guess and argue about the quality of competition and which type of homogeneous, domestic football league, was superior. That means that often times when looking at players pre-1990s, people focus on the World Cup and perhaps the Euros, because that is one of the only times we can be sure the best players played against the best competition. Of course, that is a very imperfect model, because if we focused on that in the modern game, people could be convinced that Miroslav Klose was better than Lionel Messi.
This differs greatly from American sports, where basically there is one league that is considered to be the world's best, and that league has existed in basically the same form since the sport reached the professional level. Even though the game has changed greatly, we can look at Honus Wagner 120 years ago, and easily point to his greatness, not only because we have statistics, but he played in the same baseball league, with the same general structure, with the same general teams, and the game hasn't changed so much that we can't appreciate greatness from more than a century ago. The same cannot be said for soccer, which due to being a global game, it does not have the same kind of standardized structure that we can use to universally measure players against.
In addition, even in the modern game it is hard to compare similar players across different leagues, because the talent level, schedule, and style of play all varies so much that it is hard to look at any meaningful statistics and declare one player superior to another.
Let's compare a collection of true No. 9 strikers over the past five seasons. Let's look at Harry Kane, Edison Cavani, Luis Suarez, Robert Lewandowski and Gonzalo Higuain. All of them have been playing in different leagues, and their goal totals and effectiveness are all going to vary based on those leagues, so even though they all play the same position and all play in the same era, statistically it is very hard to compare them.
Compounding all of that is that soccer has relied so much on an artistic bent and outside of goals and assists, statistics really don't have a general practicality on player evaluations, with advanced metrics starting to creep in over the last few years, which could change things. So you are relying a lot on reputation, legend and glamorization of players to really sell their greatness. I don't think Zidane belongs in the conversation, but Zidane was so elegant with the ball and played in such a unique way that he is remembered for being better than he probably was. I'd rather watch Zidane highlights than Gerd Muller, but I'd argue Muller was a significantly better player.
So I don't have a true GOAT pick. I guess you could argue for Messi, who I actually find boring due to the robotic nature of his career. His longevity and playing in an era that had a closer uniform standard of quality will set him apart, although I'd actually probably rather have Ronaldo on my team, which doesn't necessarily make him the better player.
Cruyff, Puskas and Josef Bican are among the three most influential players in history (Bican maybe not in the same way, but he is probably the most historically underrated player in soccer history, which really covers some ground) and part of that is because of their respective national teams (which really reflect an overall domestic approach to soccer) were influential and really changed the game in a way that Pele, Messi, Maradona, Ronaldo, etc. never did.
Certain players, mainly Ronaldo De Lima (Brazilian Ronaldo, aka Ronaldo Classico aka Ronaldo Fenomeno) have an argument to being the single greatest players at the height of their powers, but didn't have the longevity (Van Basten is a similar situation). Ronaldo's first season at Barcelona, before any of the injuries, is the true stuff of legend and really hasn't been equaled in a lot of ways. Ronaldo missed years with knee injuries, and was out of shape, and yet was still the best player in the world at times.
I voted for Alfredo Di Stefano because I wanted to be a little cheeky. Di Stefano, by playing in El Dorado and dominating, did play at a high level against an international cavalcade of the world's best players, despite playing in an era when that was basically impossible, outside of El Dorado. He also was probably the most versatile player in history, playing the game in a way that doesn't exist today. Someone mentioned Pele as being a player who pioneered South American players being taken seriously, but that isn't true at all. Di Stefano, when he went to Real Madrid and turned them into the juggernaut of Europe, was really the trendsetter in that regard. He probably isn't the true GOAT because Messi is better than him by virtue of being a modern player, but Di Stefano deserves recognition.
There is a great YouTube channel, HITC Sevens, who does a great breakdown on historical evaluations and the impact of past soccer players and developments that have shaped the game today.
View: https://www.youtube.com/watch?v=ERKluSLFHOo