Your viewfinder itself has no impact on AF, just your sanity when looking through it.
Now if the mirror is dirty, that could effect what you are seeing in the viewfinder and the AF. Be careful how you clean that mirror, it is easily damaged. A sensor cleaning kit isn't what you want for that.
There is another element that you see in the viewfinder, and that is the focusing screen that lies above the mirror, and that could be dirty, but also is a sensitive item to clean.
Your sensor is under the mirror and you don't see that ever in the viewfinder, nor is it used for AF when using the viewfinder, so that isn't the issue.
I would first clean the outside viewfinder glass (which your eye goes up to) with a qtip and see if that fixes things. Next take off the lens and look at the mirror and see if it seems clean. Then look up at the focusing screen with a good flash light. Before you touch any of these items, I would do some research on the best ways to tackle each item. The only thing I would try out of the gate is to buy a bulb blower and blow off the mirror and everything up in that pentaprism/focus screen area without touching anything.