My son took his son from Connecticut. Can the mom file for custody if the baby is not in the state?

Yes, as long as she files in the child's State of residence. How long has the child been gone?

If Connecticut is the child's legal residence, that's the State with jurisdiction.

If your son took the child without the mom's permission from Connecticut, the mother can rush to the court and file for custody and ask to have the child returned to Connecticut.

If he is in his new state long enough to establish residence legally in the state, he can file in his new state.

But he should have done it all though the courts first.
He may well have to move back to Connecticut and fight for custody there.

I just noticed there is ANOTHER thread, same OP, which addressed this subject very well - https://www.askmehelpdesk.com/family-law/what-connecticut-law-father-leaving-state-child-624419.html

The circumstances are not as cut and dried as it would appear - the parents had no where to go. Apparently father took the child to live with family instead of being homeless or in a shelter.