Title is self explanatory, but I will lay some ground rules.

1. This is just the Harvesters from the first Independence Day, as such their massive continent sized mother ship and other craft from the sequel will not be included in their forces.

2. The human characters from ID4 will be wholly supplanted by the Avengers and other characters from the MCU at this year.

3. Scarlet Witch, Quicksilver, and Vision will all not be included in the defense of the globe as they have yet to join the Avengers (or be created in Vis' case)

In the Independence Day universe, we are aware that when the Harvesters launched their first invasion of Earth, their City Destroyer craft targeted central, important human locations in the variety of cities destroyed globally. Within the first movie, the three locations we are shown are the White House (DC), the Library Tower (LA), and the Empire State Building (NYC). Once the attack occurs, all three locations are immediately incinerated prior to the rest of their respective cities.

Twenty years later, during the events of the sequel, we can see that many cities around the world are now fully repaired. In particular, Washington DC is shown many times. DC seemingly had almost none of its prior architecture preserved/rebuilt beyond the White House. The Capitol Building has been enlarged and changed architecturally, though still similar to the original, and the Washington Monument now includes a list of victims on its four faces. I can only assume this was a similar case in LA and NYC, but I believe that the case was different in NYC. For starters, following the attack in the first movie, we see a shot of Manhattan showing the devastation. Something worth noting is that the city's skyline is actually remarkably intact. The most prominent example of this is the fact that both of the Twin Towers actually survived (though severely damaged).

This leads me to believe that skyscrapers, of all building types, are the least susceptible (though still vulnerable) to the City Destroyer's energy weapon. Conversely, a target like the White House or other smaller structures were easily wiped out by the fire wave produced by the energy weapon. This is where NYC's target, the Empire State, comes back in to the theory. The ESB's way of destruction is ultimately the same as its sister targets, complete incineration. As such, it wouldn't be able to be rebuilt as easily as the other NYC towers due to not all of them being destroyed to that same degree. I believe that when the US government was starting to rebuild the destroyed cities and targets, they determined that the Empire would be the most logistically sensible ground zero to not rebuild and instead repurpose into a memorial. It would also make sense considering of the three cities destroyed in the first wave, NYC was the largest, 16 million metropolitan in the 90s as opposed to the 14 million in LA and 5 million in DC. Furthermore, of the three targets, the ESB would be the hardest to rebuild. The White House is an important government facility, and as such its priority would be high to rebuild to the most accurate centimeter. The Library Tower in LA was built with more modern techniques and modular capabilities, meaning it would be the significantly easier to be rebuilt. The Empire State Building though, while a beloved landmark and incredibly famous, was not a government facility integral to the functioning of the US, nor was it originally built with the more refined techniques of the Library Tower.

Tl;dr, the Empire State of the main three targets in Independence Day was never rebuilt as of the sequel and its grounds contain a memorial