The good news is that if they show up through your eyepiece then they're not on your sensor.
(I'm assuming DSLR here.)
Could be on the mirror, carefully use a blower brush. The mirror is front surface coated and VERY easily scratched.
Could be on the fresnel, this is on the underside of the pentaprism and is visible if you look into the camera through the "lenshole". if it's a posh camera it may be possible to remove the fresnel, have a look in the manual (It's in the attic with the boxes!)
Could be under the eyepiece. Remove the eyepiece, there may be a trick to this, again check the manual (It's in the bin.) and go at it with the blower brush.
If all this fails, learn to live with it as it doesn't affect your pictures and in all probability it will dislodge itself and fall somewhere less visible (But infinitely more damaging.)