The 5D MK II is known for getting dust inside the viewfinder, and it happens to other bodies as well. Its best to leave it alone, but, if you must get it out, you might need to remove the focus screen and risk getting the dust on the sensor, which is mucho worse. If its on the eyepiece side of the viewfinder, I use a q-tip dampened with lens cleaning solution.
There are a number of places that dust can sit on, the mirror, the bottom or top of the focus screen, etc. Determine where it is before trying to remove it.