NintendoWire is reporting that the 3rd and final game in the BoxBoy trilogy- titled Goodbye! BoxBoy!- will be released in Japan on February 2nd, 2017. No US release date as of yet.
Even more exciting- for me, at least- is the physical edition of the game which will include the previous two installments (BoxBoy! and BoxBoxBoy!) and will be packed with a BoxBoy! Amiibo.
Details here: http://nintendowire.com/blog/2016/12/05/goodbye-boxboy-coming-3ds-japan-alongside-new-amiibo/