If you have an Amazon prime account it's easiest to order an amiibo from Japan where there's a supply surplus, they tend to be cheapest and the shipping is free.

If you're not an "in the box" collector (it's in Japanese) they're not region locked. I've gotten most of mine that way.

Otherwise, this amiibo problem was mostly due to Nintendo underestimating their popularity and, even more so, the problems of shelf space. Retailers have only so much room to dedicate to amiibo, so Nintendo planned to always be cycling through characters somewhat quickly so as to make shelf space for the new ones.

What perplexes me is why Nintendo doesn't increase their supply and sell directly online from a warehouse. I suspect they're worried about creating and bursting a bubble, but it bums me out that a star fox amiibo costs around $30 at this point :(

Nope it's not just you. Like I said a long time ago, this is the disney vault strategy.

Maybe they should just open their own stores worldwide then.

Why can't Nintendo just sell Amiibo directly from their online store? No need for a retailer.

No, it didnt. It means that for things to go into stock, they have to be ordered by distributers whose orders come from the retailers.

Nintendo only ships what is ordered to them. If the stock isnt enough at retailers, the next order has to go back up the chain again to Nintendo. Without all the involved parties participating, it wouldnt be possible to stock amiibos anymore.

In short, retailers and distributors didnt believe there would be much demand for the amiibos and Nintendo only produced what they asked for.

Obviously, now that the demand seems to be real. They are scrambling back up the chain to Nintendo, but Nintendo wasnt prepared for it. These are the same retailers that overorder millions of Watch dogs copies. Its all due to bad management.

If i'm honest though, the distributers are the real culprits here. The retailers are very much at their mercy. Only the biggest retailers have haggling power.

Then it isn't just me. 

Because that ruins the magic of retail demand.

Nintendo responds to Amiibo shortages:

Retailers are to blame for the most part. By not limiting the ambiio's to a total of two per customer we see shortages. If people stop bitching to Nintendo to make more and start shifting the complaints at Wal-Marts , Targets, Toys R U.S, etc you would see the more stock. Its called logic Nintendo has deals with retailers its up to the retailers to keep their end.
My example is the fact every store not named GameStop has been sold out of Bayonetta in my city and not one retailers has re-ordered more. You think retailers would want to make money hmmmm game has sold out in roughly 3 months nah do not order more.

I only own one amiibo but it was a mainline one that came out recently. Not only that it was in stock for a few days before it was all gone. Nintendo needs to find a way to make it so all amiibo are like that. In shop at least for a few days before they are sold out.