What games are currently in development by Nintendo studios?

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At this point, almost all Nintendo's in house teams will be hard at work on NX projects.
Zelda U is pretty much the only current gen game still being internally developed.

(Pokken is by Namco Bandai, Twilight Princess HD is by Tantalus, Starfox Zero is by Platinum, Hyrule Warriors Legends is by Omega Force/Team Ninja)

If I had to guess I'd say that EAD1 have been working on Mario Kart 9 for NX since MK8's DLC wrapped early last year, Tokyo EAD will have been working on NX's 3D Mario since Captain Toad wrapped in late 2014, EAD2 are getting Splatoon 2 for NX underway, EAD4 will be working on Pikmin 4 for NX, Retro will be making Diddy Kong Racing for NX, and and Monolith will be assisting with Zelda U while brainstorming their next big project.