The tomatoes are still edible, but may be slightly less tender or flavorful in those areas. The best way to beat these critters is to pick the fruit at the first signs of maturity. When tomatoes begin to slightly change color from green to a yellowish-orange, take them off the vine and finish the ripening process inside, safe from the insects. They don't have to be on a windowsill. That just allows you to watch the ripening process.
Most experts actually recommend ripening in darkness by placing fruit in paper bags.
Peppers are kissing cousins of the tomato and many South Texas gardens are graced with some form of pepper. Hot peppers can be harvested at almost any time, depending on the desire of the gardener. Bell peppers are a different story. They are a little more difficult to grow and to decide when to harvest than hot varieties. These peppers do not like cool weather and therefore cannot be planted early in the spring.