I think Kid Icarus or Resident Evil have the best graphics on the 3DS. Both have a lot of impressive lighting and shader effects, and plenty of detail. Kid Icarus has more wide-open, large scale areas, though, which makes it more visually impressive.
Vita? I don't know, I don't own a Vita. I probably won't buy one for at least a couple years, either. Nintendo's games are what convinced me to buy a 3DS.