Toms ripen well on the windows sill.
Black dots on the bottom could be blossom end rot, can be worse inside the tom, so cut in half and then cut out any bad bits before eating.
If the spot starts getting bigger before they start to ripen, then I would chuck them.
Other brown marks could be blight, if it is they will get a lot worse very quickly, so quickly chuck any that are getting worse, and spread the toms out so they do not touch as one tom with blight will quickly pass it on to it's neighbours.