I’ve been struggling with your question regarding the difference between Boston and Tokyo. I guess you are referring to atmosphere which would be comprised of architecture, historic connections, people’s demeanor and other intangibles.
As far as architecture is concerned Tokyo and Boston are almost completely different. They are similar in that any fauna in the downtown area is isolated in parks. Otherwise there is very little space in between building in Tokyo. There are high-rises everywhere you look and the funny thing is that even the short building (less than 9 stories) contain shops on almost every floor. When you are walking down the street looking for some place to eat you need to keep looking up. When I first moved here I missed a lot of good places because I kept looking at street level or below.
Tokyo, obviously, has a lot of connections to history. The Alias, however, bombed the city to dust, so most of the buildings are relatively new and anything that looks old is probably a rebuild. There are lots of historically important temples and of course anything used by the Imperial household is well connected to the history of Japan.
In regards to people�s demeanor, the Japanese are everything you expect when you read about the sociology of the country. They are very kind and conscientious of their friends and acquaintances, but they are downright rude to strangers. The customer service is on the face great, but if you need anything out of the ordinary it is atrocious. In contrast to nearly the whole of Las Vegas and some areas of Boston I feel safe just about anywhere I go.
If you feel claustrophobic in crowds, never come to Tokyo. If you can�t stand 40 degree heat with oppressive humidity, don�t come to Tokyo. If you love food and are willing to experiment, but can live without buffalo wings and great bagels, never leave Tokyo. If traffic jams make your blood boil, never come to Tokyo.