First thing to check is the diopter setting for your viewfinder. Remove the lens from the camera and point it at something brightish, like your computer's monitor or the sky. Use the diopter adjustment (knob or lever, varies on different Nikon models) until the overlaid lines in the viewfinder appear the sharpest. Put a lens back on and test.
If this doesn't solve the problem, the likely issue is that the focus screen in your camera needs shimming.
Focus screens are shimmed at the factory to adjust for manufacturing tolerances, but we're talking about very small differences, so sometimes the factory adjustment isn't perfect. Also, if you change focus screens or have to re-seat them after dislodging them, the shims may no longer be in place or properly installed. Nikon makes several shims ranging from .05mm to .15mm, and they're often combined to make other thicknesses. While you can get a shim set for about US$12, re-shimming is not something I suggest most users should tackle on their own, though. It's delicate work around delicate components (the mirror, for instance). It requires patience, time, and discipline to do right, and is one of those jobs I usually leave to a good repair facility (it doesn't require Nikon authorized repair). The Nikon part numbers for the shims are 1K603-xxx, where xxx is 372, 373, 374, or 384 depending upon the thickness.
