I'm personally sticking with NMM at the moment. While Mod Organizer is most definitely a better mod manager, it updates a lot more slowly than NMM, and my experience with it and Fallout 4 has been pretty unreliable. NMM is a pretty capable mod manager (despite what I've seen some people say), and while it has had bugs, the ones I've experienced have mostly just been minor or somewhat annoying, like when it would clear plugins.txt after installing a mod (if I remember correctly) - annoying, but pretty easily solved. The bugs are normally ironed out within a few days (at most), and the more frequent updates does mean that it wasn't too far behind Bethesda changing how plugins.txt works, so if Bethesda does any changes like that out of nowhere again, I'd assume that it would support the change a lot sooner than Mod Organizer. There's also the fact that you don't have to worry about potential problems using other programs, seeing as you can launch them like normal (which could be important with how WIP some of them still are).
Once Mod Organizer and other programs are in a more "finished" state (as finished as programs for Bethesda games ever are) I'd definitely recommend switching over, but until then, I'd stick to NMM for now.