There are a myriad of reasons.

Charleston was a "power city" in the early years. Ranking 6th in population as late as 1830; 4th in the first census in 1790.

New York may be the best natural harbor in the world, the Hudson river provides great access to the rest of the state and then the Erie canal provided amazing access to the area that became Chicago and the rest of the Midwest.

Philadelphia and Boston were similarly good harbors. Philadelphia and the rest of Pennsylvania were famously tolerant, having been founded by the Quaker William Penn relatively late, in 1682. It's population grew rapidly over the next 100 years.

New York, especially during the Dutch period, was also famously tolerant.

Washington D.C. was simply a border area nobody really care for all too much, located in roughly the center of the country at the time, from which the federal government could operate.

The hearts of New York, Philly and Boston were not swampy.

Atlanta is simply not near the coast, Georgia was one of the least populated states and on the periphery of the country, and was founded far later than all the other cities you mention.

Also; overbearing heat may have been much less desirable back then, as opposed to the cold northern cities. It is pretty easy to heat a house with fires. Cooling a house in summer was far harder before A/C.

Based on the understanding I gained in a class I took in 2012 on "Atlantic" history, I came to the conclusion that the cities mentioned here (closer to the Northeastern parts of the USA) gained their power because they became the USA's financial core - where we managed our trade with the rest of the world and eventually where all the banks were.

If you start early in the colonization process (let's say no later than 1700), you'll note that much of the wealth actually generated in America was through plantation labor, but most of that wealth went to landowners. For some data, check out Engerman and Sokoloff's "Factor Endowments, Institutions, and Differential Paths of Growth Among New World Economies.", which claims massive income inequality especially exacerbated by slavery. Northeast America as a whole was less conducive to plantation agriculture from its climate alone, so its colonists found it more profitable to turn to different jobs, such as shipbuilding. So already, each part of the European colonial presence in America was specializing in different goods, allowing everyone to produce and gain more of everything. One important caveat is that the early manufacturing and food-based agriculture of the Northeast was less lucrative than plantation work, so initially it was poorer than the centers of cash crop cultivation

Now, the thing about shipbuilding is that it attracts naval trade, so the Northeast in general gains a reason to act as at least an intermediary hub linking the southern/Caribbean plantations to Northwest Europe. This is where good harbors, tolerance, and climate as Theige mentions particularly come in handy and put major financial centers exactly where they are. Therefore, while this area was initially less prosperous, its crucial financial links (as well as its more literate populace) enabled it to develop a more diversified local economy and eventually also become the center of industrial development.

While this isn't the entirety of the story by a long shot, economic specialization (especially as driven by climate and natural resources) can play a major role in this sort of divergence.

It has been noted a few times here, but I want to underline that Washington DC was not a power city at all until air conditioning became widely available. I was a long time resident, without a/c, and can tell you from personal experience once you have lived through a late summer there, you see why the congressional recess is in August. Personal notes aside, David Brinkley's "Washington Goes to War" covers this, because a/c became widely available in DC right around the same time as WWII. The population exploded at this point because of war jobs, but without a/c it would have been a different story. The similar population surge in DC during WWI left after the war was over.