Actually, there's quite a few, if you you by what you get get to via the subway. That means Everett, Braintree, Quincy, Newton, Medford and several others.
But there's a more systematic way city size is measured: MSA and CSA. Boston's MSA ( http://en.wikipedia.org/wiki/Boston-Cambridge-Quincy,_MA-NH_... ) is 4.5 million, with 4 million being defined as "urban" population. These are all places served by MBTA (which claims to serve 5 million).
Now, the main issue in the way you're looking at it is that those of us from the northeast have an entirely different view of what "urban" is. There are places in the center of Atlanta that have laughable density compared to any northern city, and the Atlanta subway system serves maybe half a million people. And yet Atlanta has a metro population of 5 million with an urban population of 4 million. The threshold for urban is very low compared to what we're used to.
The truth is that the vast majority of American cities feel like they're mostly suburban sprawl. Yes, Boston is dwarfed in size by NYC, LA and Chicago, but Boston is also roughly the same size as SF, DC and Miami. And no matter what the statistics of city-limits population say, it's has more people and is more densely populated than most other cities in the country, including San Diego, Minneapolis, Charlotte, Detroit and Seattle.
As I recall, it's the 5th largest CSA, 10th largest MSA and 4th most densely populated city in the country.