It is probably mold from the water channels inside the porcelain that remain damp in damp weather. In my apartment in the city, in the one toilet there, I get specks exactly like that, and it's a real nuisance. Although I know it is heresy on this forum, I drop a Clorox Bleach toilet bowl cleaner tab in there, and then just deal with the shortened life span of my flapper. I still get at least 3 years on each Korky red flapper before I have to replace it because of the bleach, although I probably could get more if I wasn't proactive about it.
In any event, the bleach tabs totally eliminate the black speck problem. I know when they have worn out, because I start to see the specks again, open the toilet tank and sure enough the tablet is finished. New tablet, no black specs. The problem only seems to occur in Manhattan. On Long Island, none of the multiple toilets that we have there have even a hint of mold, and I have never used any kind of in-tank cleaner. In Manhattan, in the apartment building, anything that creates a fertile ground for mold to form gets mold, despite massive Tilexing on a regular basis (e.g. underside of shower mat, between shampoo bottle and tile if it is left untouched long enough, and all the usual places, like grout, where it can form).
