Tomato

Several tomatoes currently ripening on one of my vines is still green but rotting from the bottom end, farthest from the vine. I've learned that the watering must have been irregular when the vine was setting the fruit and this caused this problem.

Colorado Springs has experienced a large amount of rain this summer. A large number of my tomato plants have stunted growth and yellowing leaves with spots. Plants in containers seem to be doing fine but the plants in my raised garden are not. Is this a drainage problem or a temperature problem?