FTP is pretty limited in what you can do. I don't know that you can unzip via FTP. You could be clevel by uploading a .zip file and then uploading a PHP file and running it in the browser where that PHP file looks for the zip file and unzips it but that's pretty hacky and may not work depending on security and permissions that are set.
I would recommend gaining SSH access to the server. With this you can `zip` and `scp` the file up, login and unzip. Even `rsync`-ing the files will be quicker than moving each file individually with FTP.