It will be a little time consuming, but the best way to protect the plants is to build small exclosures using one-quarter to one-half-inch mesh hardware cloth. You can get it at your local home supply store. You basically just make a cylinder from the hardware cloth and place it around the plant. Since chipmunks burrow, the wire needs to be buried six inches below ground (careful around the plant roots). And the top of the exclosure also needs to be covered with the hardware cloth so they don't climb up and over. If you leave one or two tomato plants unprotected, the chipmunks will hopefully focus their efforts on those plants instead of the protected plants.
Trapping is another option. You can use rat-traps to catch chipmunks. A permit is not needed.