Excuse me, but the "Mona Lisa," the "David," and the "Last Supper" were NOT controversial in the late 15th and early 16th centuries. Nor was Botticelli. There were no great arguments about their works, no censorship, no threats against the artists or patrons.
Botticelli did later, supposedly, become a follower of Savonarola and regretted his elegant pagan-themed works, but this has never been confirmed; stories about Botticelli seem largely to be myths. He did plenty of perfectly orthodox religious works as well.
Leonardo at one point was apparently accused of sodomy (homosexuality) and was acquitted, but the "Last Supper" was regarded as a great masterpiece.
And the David? It was acclaimed.
Today, there are disputes about interpretation involving the works above, but these are not great controversies, merely academic arguments.
However, if you want a painting that did involve some real controversy at the time it was unveiled, see Michelangelo's "Last Judgment" in the Sistine Chapel. The nudes set off a firestorm of outrage and criticism, to the extent that artist Daniele da Volterra was hired to paint draperies on them.