Nowadays, amiibo outside of the Smash series - such as Wolf Link or Chibi Robo - would be on the further end of the scale of rare amiibo, I'd say. Primarily because Smash is the main focus for amiibo and usually they'll cross over into other games for small rewards when used outside of that game, rather than making separate series for those instances.
On the other hand, amiibo like Wolf Link were designed for specific games, usually bundled with special editions and seldom seen elsewhere. These are much rarer because, since their games came and went, their amiibos are no longer in demand and therefore unlikely to be sold anymore.
I believe there were also certain Mario amiibo to celebrate the anniversary several years ago, including pixelated ones. I believe voxel would be a more accurate description but you get the idea. If I recall correctly, there were also silver and gold editions of the usual Mario amiibo, which would also be quite rare. I'm not entirely certain how much rarer than the aforementioned game-exlusive amiibo, though.