Chipmunks vs tomato plants
There are no easy answers when it comes to protecting your plants from wildlife damage. Here are some suggestions:
Pick your tomatoes before they are completely ripe (at the blush stage) and let them ripen on your kitchen counter. Cover the plants with floating row cover or bags. Provide water nearby and the chipmunks might go for the water and leave your tomatoes alone. You can use 1/4" fine mesh hardware cloth to exclude them from the garden or individual plants. Just be aware that these critters are persistent and may still find a way in and building a cage around each plant will make it hard for you to harvest, too.