Keep in mind that Napoleon’s first three years in power (as consul, not as emperor) were nothing but a headache for Jefferson and his Democratic-Republican Party. The Adams administration had been fighting an undeclared naval war with France under the corrupt Directory which governed from 1795 through 1799. After Napoleon overthrew the Directory, he moved to end the war and concluded the Convention of Montfortaine with the Adams administration in 1800.
The Convention was favorable to the United States and allowed Adams to present the war as a victory when he ran for reelection. Then, after Jefferson defeated Adams anyway, Napoleon began winding down the French Revolutionary Wars, secured the retrocession of Louisiana from Spain, and prepared to mount an expedition to reoccupy Haiti and New Orleans. The Jefferson administration warned that the latter would mean war.
So, from Jefferson’s point of view, Napoleon had made peace with the Federalists and was now threatening war on the Republicans. Small wonder that Jefferson regarded Napoleon’s original coup d’etat of 1799 as the betrayal of revolutionary ideals, not his later coronation as Emperor!
I’ve never read what Napoleon thought of individual American leaders. He undoubtedly had an opinion, since he had an opinion on everything, so maybe some more knowledgeable people can provide it. But I do know that Napoleon liked the United States in general. After the Louisiana Purchase the US and France were pretty much de facto allies through the Napoleonic Wars and the War of 1812, and Napoleon wanted to go into exile in the United States after Waterloo. The British, of course, had other ideas.