Enlist an artist to paint the walls with a realistic underwater mural featuring a large whale. If you are not looking for a permanent decoration, paint the scene on butcher paper or large floor-to-ceiling cardboard canvases and tack them to the walls.
Design a 3-D whale sculpture with its mouth open wide enough for children to walk into the cavity. If you don't have room for the entire whale, try having just the head placed so that it appears to come out of the underwater painting on the wall. Create a heavy wire frame in the shape of the whale and cover it with gray cloth. Add eyes and other details with white and gray cloth. Let the children sit in the mouth of the whale during story time.
Create a boat play-structure for the children to use to re-enact the story. You may make a simple boat out of a large appliance box or recruit a carpenter to build a more durable wooden play boat.
Cut a large whale out of butcher paper and leave a trap door somewhere in the middle of the whale where the belly might be. Cover the top half of a bulletin board with light blue paper for the sky and the bottom half in darker blue for the sea. Cut the top edge of the dark blue sea to resemble ripples in the surface. You may add underwater details such as other sea creatures, coral, rocks and sea weed as desired. Attach the whale in the center of the sea and place a praying Jonah figure under the trap door. Label the board with the caption, "God heard Jonah pray when he was in trouble and rescued him." Give each child a small whale on which to write or draw pictures of their own times of trouble.