What is the best ?

public void logMessage(String message){
plugin.getInstance().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getServer().getLogger().info(message);
}

Seriously though, it doesn't matter.

 

All these "get" methods are called accessors (or informally getters).
They really aren't much difference between using 1 or 2 getters.
You're fine either way
I personally would use plugin.getLogger.

 

Your Plugin#getLogger() is customized to show the name in the console so it's easier to identify which plugin sent the output.

You cannot use the Plugin#getLogger() in the onEnable method of BungeeCord, so be careful.

 

^