Updating via the plugin manager is the best and safest way to update any plugin, as WordPress will extract and set the proper permissions and the file ownerships inherit from the apache server.
Updating any plugin via FTP/SSH or other direct file upload methods is generally problematic as the client user ownership of the files are not neccessary in group with the apache server, so it may not be able to access the files afterwards. I only recommend that to developers who can set the ownerships and folder masks properly via SSH.
You can also enable automatic updates, that is the same as updating via the plugin manager.