Beating the Master Ball tier is not a very good strategy for gaining them quickly, though you also get regular Bottle Caps along the way, meaning you need less Gold Bottle Caps.
However, if you just want Gold Bottle Caps, according to Bulbapedia, the only other method is via the Digging Duo in Bridge Field. The Skill Brother sometimes digs it up, and it's not super rare apparently.
Oh, oops, and like snom said, you can get them from the Cram-O-Matic but you'll probably get the Bottle Caps from the Battle Tower/Digging Duo anyways.
Hope this helps! :)