You may appreciate this answer from /u/deleted about Chernow's portrayal of Jefferson.

For an alternate depiction of Hamilton which runs counter to Chernow's image in many ways, I recommend William Hogeland's books Founding Finance and The Whiskey Rebellion.

Well, let's put it this way: Chernow does reasonable research and is a good read but also has a disquieting tendency to massively downplay or outright ignore the flaws of his subjects - one reason, incidentally, why I consider Jean Edward Smith's earlier Grant far superior to Chernow's book of the same title. The two books were critical in launching the reevaluation of the last couple of decades of that long maligned President, but Smith was always careful to try to incorporate appropriate criticisms of his subjects.

I'll give an example: In the case of Grant, Chernow mostly just exonerates Grant from bribery personally and leaves it at that, but Smith goes far further into it and concludes that his administration was indeed a disaster when it came to ethics. However, Smith's more valuable insight is that Grant's biggest problem wasn't that he was an early version of Warren Harding (who probably qualifies as the single most personally corrupt President) but rather that he had a disastrous tendency to trust and hire people he shouldn't have who had neither qualifications nor moral standards appropriate for public office, and did a horrific job managing them - something that Chernow doesn't explore in any such depth. The same goes for his treatment of FDR; it's a laudatory biography, but Smith does not pull punches when it comes to things like court packing, FDR's affair with Lucy Mercer, or his agreement to intern Japanese Americans during the war.

Good academic historians acknowledge and incorporate the arguments of their opponents, and while I don't mean to bash Chernow - he's certainly not in the same problematic class as say Ambrose - it's not something he does well. That pops up in his treatment of both Jefferson and Hamilton especially when they came in conflict; I've written before, for instance, about how Hamilton's blatant attempts at manipulating the Election of 1800 nearly blew up the nascent United States. Whatever else you may say about him, it's really hard to excuse Hamilton's conduct during the entirety of the Adams administration; he undercut Adams at every opportunity, had full control of his Cabinet and tried (and often did) run the government from behind the scenes, tried desperately to get the United States into war with France partially to restore his own political star, considered using the army raised for that purpose to invade Virginia to do the same, and then finally blew up his own political party for what were probably selfish political reasons - all of which is barely covered by Chernow.

So rather than get drawn into an interminable debate about how wonderful/terrible Hamilton/Jefferson were that has gone on for the last couple hundred years, I'll answer your question this way: I'm glad you're reading Chernow as you're starting down a path to be able to make a coherent analysis of the men, the era, and the politics. However, the other thing I'd say is you need to read a lot more before coming to the surety behind the conclusions you have, and a good place to start might even be with our AMA on Hamilton the Musical as the musical relies heavily on Chernow as its main source material.

Then I'd recommend four more relatively recent non-academic books to start your journey: Nancy Isenberg's Fallen Founder, which portrays a very different Aaron Burr and Alexander Hamilton than who you've read about so far, Jon Meacham's Thomas Jefferson: The Art of Power and Joseph Ellis' American Sphinx: The Character of Thomas Jefferson to help you begin unraveling perhaps the most complicated political figure in American history, and David McCullough's John Adams to understand a bit more about the political context and personalities of the era.

Go forth and conquer, young mind!