Just giving a friendly word of wisdom.
So, is it after you save the file as a JPEG you see the "noise?" If that's the case, the quality is too low and what you're really seeing is posterization. A JPEG throws away similar colors to shrink the file down to a nice size. It turns the nice sky gradation into a awful mess.
Try going back and saving a higher quality JPEG and see if that fixes the problem. If the site you use only allows a small file size and that's why you're taking down the quality, my only suggestion would be to find a new site to upload your photos.
File conversion from a RAW will not add noise. Editing a non-RAW file will.
I am not sure how to diagnose your workflow to tell you how to fix your situation.