I never liked noise reduction - it always is costing the detail and i must say i like grain in high iso photographs
Also if you print big the noise is much less than on screen and on screen you do not need the high resolution ; ergo no noise... no problem..
What is see in a quick test using phase one7- capture NX2 - PhotoNinja1.03 - Photoshop ACR CS6 and DXO8 is - that i like ACR best for high ISO. PhotoNinja is worst. ( d800e)
I just did some 'normal' photos in PhotoNinja and they look better than ACR.. more real, more detail- more 3d. It fully uses the d800e NEF quality by default.
Photo Ninja uses a new version of Noise Ninja for noise reduction. I find the default luminance noise reduction settings to be too strong. The PN tutorial actually suggests manually starting with both the luminance smoothing and the detail sliders at zero and then raising them gradually until reaching the level of acceptable
noise (not no
noise). I do smoothing first and detail second. Using this method in very noisy images, I usually end up with smoothing at 8-16 and detail at around 2-3 times that value. For less noisy images, the settings are lower. I have done some comparisons with ACR, and I think that they are very close in terms of NR, but of course, the PN images look much better overall.
Why don't you try this method, and let us know how it works for you?