If it works with your router, DSFTP is the better of the two. Lilou's Combox (also known as CFTP) is a lot more buggy and a lot more complicated (although it can work as an FTP client as well as a server and has several other features as well). I don't know of any other FTP clients or servers for the NDS.
Both DSFTP and CFTP are quite slow due to the limitations of the WiFi. Both have the potential to corrupt your microSD if you don't shut them down properly before rebooting your NDS. Frankly, it's a lot faster and easier just to use your microSD reader to transfer files to/from your microSD card.
-Bri