Since you're using vuescan why not just do multiscanning. I think that will have the effect of averaging out the detector noise, try it. If not then you can manually average out a few separate scans. For every two scans you average, I guess the signal to noise will improve by sqrt(2) or so.
Noise Ninja will remove noise at the expense of detail, that's all it can do. Multiscanning & averaging can remove detector noise without sacrificing detail.
Of course the other thing you could do is overscan and then downsample. but again this is going to lower detector nosie at the expense of some detail.