The boys, who live with their father in Vernon, were unharmed, Vernon Police Detective James Grady said. Their mother, Jackie Morris, 32, could face criminal charges in Connecticut.
"The father is very happy his children are all right and that is everybody's concern," Grady said.
Bangor detectives found the boys, aged between 7 and 9, shortly after Vernon police issued an Amber Alert. Morris was also at the motel.
Morris has apparently been living in her car recently, Grady said. He said police had had previous contacts with her.
Connecticut child welfare officials were working out how to return the boys to their father.