I would choose Maddalena Doni because it shows how he uses cool, crisp colours in his art. Also it shows how he used accessories to show off the status of the sitter unlike Leonardo da Vinci who would make the status of his sitter ambiguous.
However if you wanted to look at his transition from High Renaissance to Mannerism I would go with either Sistine Madonna or the The Transfiguration as they show aspects of both styles.
