If you own a Vita OP, you have some more options to consider across native Vita games, PSP titles and PS1 titles:
-Tearaway (Vita)
-Ratchet Collection (Vita)
-Sly Collection (Vita)
-Sly 4: Thieves in Time (Vita)
-Jak Collection (Vita; Only consider this if you can deal with bad frame rates)
-Daxter (PSP)
-Dead Head Fred (PSP)
-Death Jr. II (PSP)
-Jak & Daxter: The Lost Fronter (PSP)
-Ratchet & Clank: Size Matters (PSP)
-Secret Agent Clank (PSP)
-Toy Story 2 (PS1)
-Pac-Man World (PS1)
-Gex 2 & 3 (PS1)
-Crash/Spyro (PS1; Only if you are in EU/JP PSN)
A lot of older games and few new ones (not to mention sometimes mixed quality) but most of the games I listed are good/great and play fantastically on Vita. Never expected to have such a collection of platformers to dive into when I got my Vita, my favorite game genre XD!
Regarding the main topic, the only 3D platformers I can think of for the 3DS (3DS and DS games) are the following:
-3D Land (3DS)
-Rayman 3D (3DS)
-Sonic Lost World (3DS)
-Jet Rocket 2 (3DS)
-Mario 64 DS (DS)
-Tak the Great Juju Challenge (DS)