No, only with a DSi.
And even then, it would be very hard to find one that is either hacked, or can be.
Besides, from what I read, it's even free to download on those systems ...
It is available from My Nintendo rewards and is called Flipnote Studio 3DThere is no way anything downloaded from NUS Downloader can be played on any console.
That being said, Nintendo said that Flipnote Studio is getting upgraded for the 3DS, and we haven't seen it yet if it's not Swapnote.