Yes I think you can but in order to do this you would need to have two separate Nintendo Network ID's for each console.
This is on Pokémon Bank's FAQ:
"On December 10 of this year it became possible to use Nintendo Network IDs in the Nintendo eShop. If I have several systems from the Nintendo 3DS family, can I register the Nintendo Network ID that I used to purchase Pokémon Bank on my other systems as well and thus use the same Pokémon Bank on several different systems?"
"No, you cannot. It is true that you can use your Nintendo Network ID in the Nintendo eShop with your system from the Nintendo 3DS family, but while this Nintendo Network ID can be shared with your Wii U system, it cannot be shared among multiple systems within the Nintendo 3DS family."
This is on Pokémon Bank's main page
"Only one special Pokémon is available per copy of Pokémon Bank. Even if you store Pokémon from multiple games, you can get only one Celebi!"
Hope I helped :)