The trouble with that list is that it's area-wide, so it doesn't make a whole lot of sense to put Guttenberg, which is a few city blocks in size, on the same list with NYC or Boston.
For transportation purposes, you want to look at more specific levels of density along the corridor of interest. Block-level, blockgroup-level or tract-level (census terms).
I also prefer dwelling units per net acre. Why? Because measuring the number of dwelling units tells you how many people can live comfortably in an area. A higher number of dwelling units per acre usually corresponds to less overcrowding because it is easier to get an apartment, so it is less likely that people are forced to live together unsafely. Net acre means per acre of land zoned for residential use. So this excludes roadways, parks, commercial and industrial zones. I think this is important because it is the land where people live that primarily generates customers for the transit service, not the adjacent park (though of course, it does get users too).
Under this lens, the most densely populated areas of Boston are the Fenway (100-200 dwelling units / net acre), north side Beacon Hill (100-200 du/na) the North End (90-180 du/na), Back Bay Comm Ave (75-150 du/na), Allston/Brighton Comm Ave (60-120 du/na), Southie W. Broadway (110 du/na), and the South End (50-200 du/na).
Most of Dorchester and Roxbury falls in the 10-40 du/na range, as does Brighton Center. Oak Square is 10-20 du/na as is most of JP. Typically, younger suburban towns are under 10-12 du/na, and 10-20 du/na is considered semi-suburban or borderline.
Of course that is only one axis to look at, and there's a lot of different history in the various neighborhoods and patterns of usage and growth to account for too. But fundamentally, you want to build transit where the people are (or where they will be) and Comm Ave has a lot more people living there than the Cambridge/Washington St corridor.
I was concentrating on zip codes as a means for measurement and just using the Wikipedia list as a reference point - compared to the vast majority of developed areas in the United States, the inner core of Boston (with a city average of around 13K/sq mi) is significantly denser on average, yet there are certain areas that are out of comfortable reach of rapid transit.
There is certainly a correlation between overall population density and dwellings per net acre, but it does not seem to factor in higher occupancy per dwelling, does it? While the Comm Ave corridor is no doubt home to a large chunk of Brighton's population, there is still a significant portion outside of a comfortable 1/4-mile walking distance from regular rapid transit. Restoring the A Line or running light rail along North Beacon would bring the lopsided density back towards equilibrium as it brings with a significant amount of development and greater density (esp. North Beacon area).
Here's a sampling of 25 Metro Boston zip codes and their densities from 2010:
DENSITY (2010) ZIP AREA
63,135 02113 North End
36,211 02115 Fenway
27,933 02116 Back Bay
25,340 02118 South End
24,819 02108 Beacon Hill
21,667 02139 Central/Inman/MIT
21,274 02446 Brookline-North
21,069 02144 Somerville-Davis
17,817 02145 East Somerville/Magoun
17,334 02141 East Cambridge
16,129 02143 Somerville-Union
15,460 02140 Cambridge-Alewife
15,276 02134 Allston
14,620 02150 Chelsea
14,498 02135 Brighton
13,539 02127 South Boston
12,672 02138 West Cambridge/Harvard
12,080 02129 Charlestown
9,073 02130 Jamaica Plain
8,358 02453 Waltham-South
7,245 02472 Watertown
5,625 02445 Brookline-South
5,285 02132 West Roxbury
4,992 02109 Financial District
4,048 02452 Waltham-East