dark spots are much more troubling.
the best way to deal is prevention ... rap your tank well and avoid using acid stop baths when developing. I just use a plain water stop to avoid the nasty acid pinholes. But I guess this isn't very helpful to you right now!
So, there are 3 things you can do ... both of which have their drawbacks and need a bit of practising before you get proficient at them:
1. Spotting the neg before printing. As the pinhole is clear in the neg, you can spot the neg using your spotting inks to turn it into a white spot on the print, which can then be re-touched to the correct tones
2. Knifing the print. The black spots are actually slightly raised in the emulsion. With great care, these can be removed with a fine scalpel blade, leaving a white spot which can then be re-touched using the spotting inks. It is really hard to do this well invisibly.
3. Bleaching the print. Using something like farmers reducer, or iodine tincture, you can apply a small drop, onto a wet but squeegeed print, using a fine brush or cocktail stick and leave it to take the black spot back to white. - wash (+ fix+wash again if using iodine) then treat it like any other white spot on the print.