Hi Persian,
I'm not sure which camera you have but if it has interchangable screens then that could be part of your problem. The screen sits under your pentaprism and in some models can be changed for different effects, eg horizontal & vertical lines to help with architectural /tilt shift images. Anyway, back to the plot, when using an Eos 3 I had a similar problem to the one you describe, cleaned the mirror using a sable brush (yeah i know, dont do it), cleaned the underside of the focussing screen but still had this huge thing in the viewfinder (that'll teach me to change lenses on a windy day in the middle of a cut field of corn). So, I took out the interchangeable screen and there was this 4mm piece of corn just sat there, blew it off and reassembled.
To do this I used the canon tool for swapping out screens, the screen has a little lug on its side which the tool grips in a sping loaded vice, DO NOT TOUCH THE SCREEN only hold it via the little lug otherwise you will get crap onto the screen and as it is a frensel lens (I believe) which is covered in lots of little grooves, getting finger grease into them would not be a good idea. I would suggest popping down the screen mount, using your blower brush to clean it out and then just remounting the screen so you dont even need to take it out of its mounting.
Hope that helps
BearSummer