I agree that a jack russell or any sort of small working terrier would be the most effective long term deterent. However they may dig a hole to china to get at them!
For all practical purposes a good pellet gun would be the most effective tool over time. The crossman/Benjamin Marauder .22 cal with scope will reliably hit a nickel out to 50-60 yards. Because they are a "pre-charged pnuematic (PCP)" gun, they are extremly quiet and poweful and IMO easier to shoot accurately out to these distances. They cost about $400.
That being said, no matter what you do, I don't think you'll ever get rid of all of them. Chipmunks are usually harmless in small quantities, but can be destructive if the population gets out of control.
One more thought, just make sure you don't run afoul of any local or state laws regarding chipmunk control. Also for shooting pellet guns around town. Some states have laws about this.