Is Jerry the antagonist as well as the protagonist in "Through the Tunnel"?
Not every text necessarily has to have an antagonist. Of course, you are right in identifying the protagonist as Jerry. It is he who is the main subject of the story and we follow his journey from being a child to becoming an adult. However, your question does raise the importance of internal conflict to this story. Jerry is a boy with something to prove, and as he chances upon the tunnel, he finds a way of proving to himself that he is an adult and has metaphorically gone "through the tunnel" from childhood to being grown up.
Thus it is in the tale that Jerry has to overcome his own internal conflicts--both physical and psychological--in order to succeed in his test of manhood. Note how hard he has to practise holding his breath:
First, he thought, he must learn to control his breathing. He let himself down into the water with another big stone in his arms, so that he could lie effortlessly on the bottom of the sea. He counted. One, two, three. He counted steadily. He could hear the moment of blood in his chest. Fifty-one, fifty-two... His chest was hurting.
One of the physical challenges he must face is learning how to hold his breath for longer, which gives him bad nose bleeds.
Thus you might find it helpful to think about your question in terms of the internal conflicts in the story, rather than identifying a non-existent antagonist.