Is Shantae even indie? Wayforward likes to pretend they're indie, but they're more of a middle sized developer, they land a lot of fairly large licenses to make games. Like Batman and Disney.
I think Cave Story or Bit Trip are the two biggest Nintendo indies, as far as being iconic indie series that are also iconic as being Nintendo focused series. They're also both old at this point.
Remember, it's Bit Trip that has a trophy in Smash already. Bit Trip started on Nintendo. Charles Martinet narrates Runner 2. Bit Trip is known in Japan.
I'd honestly would pick Commander Video if I was selecting an indie rep. When I think of Nintendo indies, he's the first that comes to mind.