I smoke squirrels as well as grill them. Wrap in bacon, with just a little garlic and salt/pepper, smoke at 190 until they are 168 to 170 internal. Using oak or mesquite on them is my favorite. Great stuff. Never done a chipmunk, but they would definitely be small, about the sixe of a turtle dove. Definitely have to wrap them in bacon as well. The dogs, coyotes, bobcats, hawks and eagles sure like them around here. I am sure they hunt and take more than I could evr desire.
None of these critters are cute to me. They destroy property in a big way. And there are so many of them and adapt to new obstacles so easily. It would be hard to believe they would ever be gone from the landscape. I use a .22 Marlin on them, a shotgun would be a real mess. Sometimes I get out my air rifle, but not that much anymore. My grandson still prefers the air rifle and not his Cricket 22 for the squirrels.