Nintendo recently posted instructions to their YouTube channel on how to perform a system transfer between the standard 3DS and the soon-to-be-available New 3DS. It is a little complex, with a lot of menus and the use of a screwdriver, but overall it’s not overly difficult. The process will allow you to ensure your New 3DS is linked to your Nintendo Network ID and will transfer over all of the information saved on your SD card, so you don’t lose anything upon upgrading to the new system. The 3DS and its New successor have a menu option that will perform the main system transfer, after which point you will need to plug the SD cards into a computer to physically copy the data from one to the other.
That said, the video does briefly show a “wireless transfer” option in the 3DS system transfer menu, so perhaps a simpler, if slower method is available.