Your tomatoes look really quite good. One of the dark spots may be due to a slug trying to get into the tomato and the little indentation mark on the other could be anything. It is hard to tell from the photo. If the leaves look good, you are lucky since it is nearing the end of September. At this late date, I wouldn't worry about any disease problems. If any leaves do look diseased, remove them and place them in the trash. Do not compost them. Here are two links to check over on disorders and diseases of tomatoes:

• http://www.extension.umn.edu/distribution/horticulture/M1274.html
• http://www.extension.iastate.edu/publications/pm1266.pdf

Since they are grape tomatoes, I would have thought the holes were too small for slugs. I've attached a plant picture to show overall health; I haven't found one bad leaf on this plant. It has been great until about 2 weeks ago when I started to get some with indents of white or black spots. Would the leaves look bad if it was bacterial? Is that why it can be ruled out? 

The problem might be due to bacterial canker, which is a disease that can affect the fruit and later the foliage on vegetables.  Read the section on bacterial canker that states that the disease can affect vegetables at any stage:
http://vegetablemdonline.ppath.cornell.edu/factsheets/Tomato_Bacterial.htm