The view through the view finder in any type of slr, digital or film, is an entirely optical pathway, ie through the pentaprism, and out through the lens via the mirror. The sensor doesnt come into it. The spots are therefore likely to be on the view finder glass, possible the focussing screen (the bit of glass in the roof of the shutterbox above the mirror) or mirror, or on/in the lens itself. A systematic check of these should sort your problem out.
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