They both have advantages and disadvantages.
Nintendont:
+ Easier to use since you just install it like any other homebrew
+ Doesn't hijack your MIOS slot
+ Can use nearly whatever USB controller you want
+ Has memory card emulation (better than NMM) which works well for nearly every game that's compatible
+ Has less hard drive/USB restrictions than DIOS MIOS
- Requires a controller.ini to use said USB controllers, so some manual setup is needed if you don't have one of the 'default' controllers
- Less compatible and stable with games than DM right now, due to its young age
- No wireless controller support yet (DM doesn't support them either, and never will)
- No streaming audio support yet
- No real memory card support yet
DIOS MIOS:
+ More compatible and stable than Nintendont
+ Supports real memory cards
- Has more hard drive/USB restrictions than Nintendont, so it's harder to get working
- Provides a way to save game saves directly to USB/SD, but in a weird file format, and has very poor compatibility (or it did last time I used DIOS MIOS), so real memory cards are pretty much required
- Only supports Gamecube controllers
- Hijacks your MIOS slot