I was going to take photos one day and noticed these green/brown spots when I looked through the viewfinder of my Nikon D3200. So I took a couple shots to see if they showed up, but they did not. I know that they are on/in my camera because even when I take the lens off I see them. I've tried cleaning the mirrors in the camera and the little eye piece, and neither have helped! I'm freaking out please help!
The eye lens (ocular) of the viewfinder frequently gets smudged by handling the camera or even from eyelashes. Cleaning the ocular lens is easy, as you've already done at least the outside (just use lens tissue, possibly with a drop of lens-cleaning fluid on the tissue, not on the lens itself). If the ocular unscrews, you might clean the inner surface, though it's probably not dirty.
Cleaning a mirror or focusing screen is nontrivial:
The mirror is a first-surface reflector, and even though overcoated with SiO, it is easily scratched. Check your handiwork to see if you've left streaks on it.
The focusing screen is even more fragile than the mirror. It is more likely to be damaged by removal, handling and attempted cleaning, but there is some advice on Photo Stack Exchange, and instructions at Shimworld.
Though the smudges are annoying, they don't affect photo quality, so be careful not to destroy a camera that is otherwise functional.