Black, unremovable dots are probably bad pixels in the sensor. These are parts of the sensor that no longer react to light. If you don't see any issue looking through the viewfinder, then the sensor is messed up. Since you say you don't see anything on the surface, I assume the optical part of the camera is in tact. You can try cleaning the sensor - Menu - Setup - Clean Image Sensor - it certainly can't hurt.
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