Remove the lens of your camera, do it in a clean room, look at the mirror insie the lens to see if the dot is not there rather that on the outside of your viewfinder.
If it is not there it might be on the inside part of the focusing screen. Still inside the camera look at the upper part of the body, the focusing screen looks opaque.
If you still cant find the dot it might be on the inner side of the focusing screen.
Here is a tutorial on how to remove it on a d70 it is essentially the same thing on your camera.
Otherwise it can also be on the inner part of the viewfinder. In this case I recommend to send the camera to a repair shop as the removing of the viewfinder seems to be more difficult on the d3000 than on other camera.
Hope this helps.