Air rifle and a little patience. When you see one go into its hole, sit about 5 yd away with your gun ready. More than likely the critter will pop its head out of the hole within a few minutes. This method is lethal with a scoped air rifle!
If you don't want to shoot them, but a couple of Victor rat traps, bait with peanut butter and a pecan or some other nut stuck onto the PB, and set the trap outside of the chipmunks hole. That is also effective but I prefer the air rifle method.
Remember you can't just go out and hunt chipmunks... They gotta be doing property damage. Ever since one got in and chewed through an air duct, they have been high on the hit list in my yard.