Or would they have to have their own town since it's a different acnl cartridge/download? My sister is getting her own 3ds and animal crossing game.
There is no multi-console multiplayer with one cartridge in AC:NL.
If she wants to visit your town, she'll need her own console and her own cartridge. That's the only way to play "co-op".
She will have her own town. Each cartridge will have one town's data saved to it so, unless she makes another villager on your cartridge to play when you are not, she will have to be mayor of her own village.
There will be a lot of advantages to this, though, as your sister can decorate her town as she wants and you will be able to have 10 different villagers each (there's a few hundred altogether so it will give you a chance to meet twice as many at once) so you will get more enjoyment out of the game. You will be able to visit the island together when one of you visits the other so you will be able to partake in the minigames together and if she has a different town fruit to you, you will be able to trade fruit and make more money that way. If you make money easier, you can help contribute to her public works to get her started and someday she will be able to contribute to yours.
If she is quite young and you want to help make the game easier for her then you can always dig/plant/water flowers in her town to help her out when you visit :)