Even on a 5D ISO noise is a challenge. I use PS raw photoshop and Adobe Bridge. I want to minimise loss of image quality.
What is the best way to reduce high ISO noise?
Put more light on the subject when you shoot it.
Noise is not a property of a specific ISO, it is a property of the Signal-to-noise ratio. By increasing the signal (adding more light) you can reduce the exposure which also reduces the influence of noise by increasing the signal-to-noise ratio.
Image info: ISO 3200, f/2.8, 1/1600 second. The subject was bathed in the bright light from a spotlight.
Same set, same camera and lens (although at 70mm instead of 200mm). ISO 3200, f/2.8, 1/320 second. The subject was on a much darker part of the stage. Even with the 2 1/3 stops slower shutter speed there's still less light entering the camera and the image is noisier. Using more aggressive noise reduction reduced the fine detail in the image.
When taking pictures of static objects (buildings, landscapes) you can use image stacking. By taking many pictures, aligning them and averaging over the aligned images, you'll average out the noise. Noise reduction should then be turned off, as that will allow details that are hidden under the noise floor to emerge. Noise reduction should be applied after averaging over the pictures.
When shooting under dark conditions the long exposure noise reduction should be enabled, as this performs a dark-frame subtraction, removing the hot pixels. Taking one dark-frame exposure yourself to use that multiple times to save time is a bad practice, because the dark-frame will itself contain noise that you want to average out as well.
Each picture should be taken by the "exposing to the right" method. Here you expose to the limit where you just avoid overexposure. In post processing you can then reduce the exposure which then reduces the noise. E.g. suppose that by exposing to the right you can increase the exposure by 2 stops. This will then reduce the noise by a factor of 4 in each picture. If you take 25 pictures and average over them, then that will reduce the noise by a factor of square root of 25 = 5. So, you can reduce the noise by a factor of 4*5 = 20 just by taking the effort to take more than one picture and exposing for longer.