To find out what the rarest Amiibo are, you'll want to search for them and then arrange by price. That's because the rarest ones are going to be the most expensive for the most part, due to how little they made of them. There is actually a rarity chart that can help based on what Nintendo released and in what amounts.
A lot of people assume that eventually, Nintendo will release a second wave of each Amiibo because Nintendo indicated they would release some again. That would be great due to the scarcity because re-sellers are trying to make a quick buck off of fans that really enjoy the Amiibo characters. However, Nintendo says they are limited so that probably means re-sellers are going to buy them again and do the same thing, just at a slightly lower price.
1 - http://www.ign.com/wikis/nintendo-amiibo-figurines/Amiibo_Rarity_Guide
2 - http://www.hardcoregamer.com/2015/05/15/nintendo-announces-re-release-of-certain-rare-amiibo/149061/