If it is a small mark, one of the old techniques was to use a sharp stylus or a needle perpendicular to the negative to stipple the base side of the negative over the mark. I've done this for pinholes and similar kinds of problems. Work with a magnifying glass and put the negative on a light table.
If you decide to try it, practice on a scrap negative or two first (you might even make a pinhole on the emulsion side and then try the needle technique on the base side for practice).
If the mark is too large for that, or if you try it and it doesn't work, I'd go with Donald's method of retouching the negative and then the print.