Baby chipmunks are called young..
It would just be best if you called them baby chipmunks. That way everyone knows what you're talking about. You may also call them kits or cubs. Pups are good too.
The common name originally may have been spelled "chitmunk" (from the Odawa word jidmoonh, meaning "red squirrel"; c.f. Ojibwe, ajidamoo). However, the earliest form cited in the Oxford English...
It started as a nickname given to him by an younger boy on the estate where he grew up, referring to the unusual shape of his teeth.
He chose to use the name Chipmunk after the younger boy was killed...