Leaving aside any personal opinions about the relative "goodness" of their accomplishments, the facts favor TR by a mile.
If he had never become president, his biography would still rank among the greatest Americans. Then he was a 2-term president, who won reelection by the largest landslide ever (to that point). His accomplishments redefined America both in foreign and domestic policy, and his inclusion on Mt. Rushmore demonstrates the respect still shown him.
JFK, on the other hand, only got put on the half dollar because of the tragic circumstances of his death. While we all like to project what might have been onto him, both Jack and Bobby's tale is one of potential more than genuine accomplishment. Teddy, love him or hate him, was likely the most significant senator since LBJ. But all three combined pale by comparison to TR.