I realize you may not appreciate my answer, but my suggestion is to gradually learn to ignore the spots. I suggest this because (1) they do not affect image quality, (2) they are hard to remove, (3) in trying to remove them you are likely to add more spots, or worse perhaps even scratch the focusing screen.
When I first noticed spots inside my 1D II and 5D and realized they would be hard to clean, I was rather frustrated too. They seemed to distract from my looking through the viewfinder. But eventually I just learned to ignore them. When they get overly bad, I'll send the units to Canon for a standard clean/checkup.
Eric