Depends. Both offer additional things. E.g the community patch project makes use of some nwncx features for additional bug fixes. Also, there are some camera hacks available with nwncx.
Neverrun on the other hand offers a lot of options to sort your games and servers.
Imho, you can run them both, so it isn't even an 'either/or' question.
If you do not care about any additional features, it's merely a matter of preference which you like more. Nxncx integrates itself seamlessly, the game looks and behaves nearly the way nwn used to in the old days. Neverrun on the orher hand offes a much more modern interface for browsing modules and servers.