The Japanese Amazon store has listed a special edition of Shovel Knight on 3DS that comes bundled with the game's Amiibo. The package currently costs ￥3,083 (roughly $29) and is due to release on the 30th of June. There is currently no information on a North American release, but both the game and Amiibo are already available in the west as separate items. The Shovel Knight Amiibo unlocks the ability to customize your avatar in the game, and in the Wii U version it unlocks two player co-op.
Source: Amazon Japan