When Nintendo first announced the Skylander like Amiibos, they never said that there would be a limited run on some of them. It seems that is the case though.
Confirming with Wired, certain Amiibos will have a limited run while some will always be available. You can probably guess which Amiibos are never going to go away, but there might be some already done being produced.
The Wii Trainer, Marth, and Villager are the three that seem to be very hard to find and are going for higher than normal prices on eBay. If you find one in the wild, it'd be best if you pick it up considering Nintendo is probably done making them.