Looks like a bacterial disease to me; bacterial speck can affect the fruit like that.

Speck likes cool, wet conditions, so things may improve as the weather warms up. Try to thin out the foliage some to allow for better air circulation, and try not to get the plants wet in the evening when they won't have time to dry.

If you need to spray -- and you may not, as it just makes the fruit look a little ugly, though it's fine to eat and ripens normally -- a fixed-copper spray works pretty well on bacterial speck and spot. It's organic, but not particularly healthy for people, so make sure you follow the precautions on the label if you apply it.

If it were my tomato, I'd improve air circulation as much as I could and wait it out. It won't kill the plant and it just puts little spots on the fruit. Once the weather warms up, it may go away.

--Alison