Exactly how Monster Hunter-esque do you want it to be? Do you just want a game where you take quests to beat monsters and get their stuff body parts? Or do you want gameplay that is similar to Monster Hunter as well?
Master of the Monster Lair is a DS game in which you build a dungeon to attract monsters, and then accept quests to bring parts of those monsters (or bits of equipment they're wearing) to the villagers in your town. It's part of the Dungeon Maker series (in Japan and Europe, it's actually called Dungeon Maker, IIRC), but it's a lot more RPG than either the other Dungeon Maker games or Monster Hunter, both of which have more action-oriented gameplay. If you have a PSP, you might want to check out the other Dungeon Maker games, which definitely fit the Monster Hunter style a bit better.
Dragon Quest IX has a similar system, where NPCs will frequently give you quests to kill monsters, but the quests are about other things just as frequently, and the game itself doesn't focus on the killing of monsters and the taking of stuff body parts. Also, it's a "pure" RPG, not a hybrid action game, like Monster Lair above.
Other than that, I can't think of anything besides the actual Monster Hunter games coming out for 3DS.