Of course I only use Noise Ninja when needed. But if it is, I use it first. It tends to reduce detail and therefore you may want to add a bit more sharpening than usual.
I do Input Sharpening right away. This is basicly a mechanical step, with the only decision being which level to use.
If I've used NN, then I'll apply a bit of creative sharpening, but otherwise usually not. What type to use is a highly personal decision and also one based very much on the particular image one is working on.
Then, after all the editing is done I save the image.
When I want to print, I load the saved file and apply whatever level of Output Sharpening the file needs, based on the print size and paper used.