It is wonderful that this kid is so passionate about his interests. He clearly has a lot of drive and took a novel approach for his science project- it looks like he did a fantastic job putting it together. His poster is 3 sheets long!
Having said that, though, there are a couple of major flaws with this. First, his basic premise is simply not science: pick a constellation, pick sites that "fit" the distribution (what's the scale? which sites are the ones that fit this pattern?), and then discover a site where one star/site is missing. For every site that is included on the map in the article, there are hundreds of others that are not, and at least dozens of other sites of an equal or greater size that aren't in this constellation pattern. Using this same methodology I could choose a constellation, say Gemini, which the ancient Maya viewed as a pair of copulating peccaries, and overlay it on a map and find enough sites to fill it in. I could probably make a giant smiley face while we are at it. All this would establish is that there is a high enough density of sites across an area that you can connect the dots how you see fit, but this doesn't say anything about how they saw the world.
Secondly, he may have 'discovered' a site- I can't tell if he has or has not from the article. There are thousands of sites still out there that haven't been registered, many of which are known to local populations. So he may have found something new, and that in itself would be an incredible contribution, especially from someone his age. But if his new site is in the Belize River Valley, which it looks like it may be from the map, you can't throw a rock in that area without hitting an archaeologist. That area has been intensively studied for decades and there is unlikely to be an unknown major site anywhere near there.
Finally if this new site really has a 86 meter tall pyramid in it, then we are going to have to rewrite all the textbooks since we have a new record for tallest pyramid in all of the New World, bumping out the Pyramid of the Sun. I don't think this is very likely. I would believe that he found a pyramid built on top of a hill that together reach that high about the valley floor, or that the pyramid is actually a natural hill. All of this would be quickly resolved with a visit to the site, which is why archaeologists always ground truth remote sensing imagery before going public.
tl,dr: My money is on the kid identifying a real site on the satellite imagery, whether it has been previously identified and registered or not. It just doesn't have a 86m pyramid on it, and it isn't in that location because of some constellation.
Source: I'm a Mesoamerican archaeologist doing this stuff for a living.
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The whole thing is a mess -- a terrible example of junk science hitting the internet in free-fall. The ancient Maya didn't plot their ancient cities according to constellations. Seeing such patterns is a rorschach process, since sites are everywhere, and so are stars. The square feature that was found on Google Earth is indeed man-made, but it's an old fallow cornfield, or milpa."
