No, you're misunderstanding the point.

Your graph is how far they are from the downtown of the largest urban center in their region. Not the population density of the area where they are.

You're entirely correct - most airports are not as close to the largest city center of the metro area as Boston's.

However, this doesn't mean that they aren't located in a dense urban area regardless.

For example, your graph says Newark Airport (EWR) is >10 miles from the city center of NYC. Sure, this is true.

However, it's located right next to two of the largest cities in NJ, Newark and Elizabeth, with the runways coming within 2 miles of both of their city centers, and high population densities to match.

Broadly, this is very similar to the environment of East Boston and the level of impact on the population, and certainly as much "within the heart of a city neighborhood" in terms of location as Logan is.

The same is true of NYC's other airports and my other examples.