I thought about gold, silver and copper too, but that sounded a bit too common, and those three don't differ enough, so that characters would accept copper but not gold, for instance. But one of these could be used as the higher level currency, perhaps.
I'm thinking acorn or other types of nuts for the lower level currency, feels like it would be something easy to carry around as if it were money, and you just had to search for the right trees.
Some kind of semi-rare gems, maybe you even would need a specific tool (like a pickaxe) in order to obtain them.
I would rather not have actual money in it, though, for me it feels like it wouldn't fit the Knytt universe.