Definitely New Threat. As difficulty mods go, it's the first that's really felt like an update to the game rather than just a tweak to numbers. Solid, consistent mechanics all around.
One thing to be aware of - if you install it through 7th Heaven, don't use Menu Overhaul alongside. Because MO uses a custom .exe, it creates some bugs with New Threat (exe changes from an older version of the mod snuck into the MO exe). That's due to be fixed real soon, but for the moment, New Threat and Menu Overhaul basically aren't compatible.