I am assuming you are referring to the new GUI system available in the 4.6 beta.
If you are already using NGUI on a project I would recommend you just stick with it. While Lyashenko (NGUI creator) did work on UGUI system during his brief stint as a Unity employee the two systems are not identical. Currently there may be a few features NGUI has that may be worth keeping it around for.
If you are considering which to go with for a new project, the biggest factor is that 4.6 is still technically a beta release. While it seems pretty stable, doing production work on beta software is always a risk and we don't know when it is going to leave beta.