I heard back from Marilyn Cox at www.imustgarden.com who has the organic pest repellents. She has one for squirrels.
"Yes, the squirrel repellent will work for your chipmunk problem…I’ll send you some samples if you’d like. And yes, they’ll eat fruit and veggies and seeds. If they burrow near foundations and patios, that can be problematic."
Check out her website. The ingredients in her products are safe and organic. Things like lemon grass oil, peppermint oil, clove oil.
I haven't had an issue with chipmunks, but squirrels are eating everything in my raised beds. Does anyone have suggestions for building a cheap cage around a small raised bed? I would love to know what type of materials to use, where to get them for a good price, etc. Thanks!