Nintendo also pimped out Shovel Knight quite a bit through the Indie sections of Nintendo Directs and E3 presentations, so by and large, a lot of people at least think of it as a Nintendo centric game. The asthetic doesn't hurt either.
The Shovel Knight amiibo isn't being made by Nintendo, they are lending tech support so that it can be a functional third party accessory, but the manufacturing is being done by a completely separate company (just like the Skylanders amiibo).
Really? Huh. Well, I read an interview with people from Yacht Club where they talked about being approached by Nintendo and asked about doing it. And the Shovel Knight Amiibo's up for preorder on Nintendo's store, which I think makes it the only third-party merch available on there. So there's obviously some Nintendo involvement going on even if they're not directly handling it.