I started looking at Boston for a DFRPG setting -- been living in New England for about 30 years, Boston area for about 20.  A couple themes that should really stand out:

 - Someone mentioned traffic.  The roads are incomprehensible, traffic is terrible, construction is arbitrary and capricious, public transportation is iffy even before you take the problem of Wizards shorting out MBTA fare readers into account ... great Compels to frustrate investigators trying to pursue a villain, or to try and get anyplace quickly.

 - Many provincial communities rub up tight against one another. Chinatown, the North End (Italian), the South End (mostly gentrified gay community), Beacon Hill, South Boston/Dorchester (Irish communities), Allston/JP(Jamaica Plain) (student ghettos).  Add in the most recent wave of academic and financial experts from around the world (Indian, South American, Chinese, European, Russian) that work in the city, and you have Boston.  There's not much left in the way of really "bad" neighborhoods, and organized crime doesn't seem to have much of a grip on the city these days (but maybe I just have my head in the sand).   But the character of Boston is maybe two dozen or so communities that live largely separated from each other and don't mingle. These communities don't fight outright but they don't really get along either.  Racial/cultural/class discrimination among provincial Bostonians is many-layered and complicated.

 - The long academic history of Boston demands antiquarian societies and restricted university libraries that are packed with arcane knowledge.  Besides fragmented private collections, there's got to be an in-depth library tucked away somewhere buried in the basements of the Harvard campus buildings.  Then there's the archives at the Boston Public Library.  On the other side of the Charles you've got MIT.  Though magic and technology don't mix, there's bound to be folks fascinated in studying magic by applying scientific principles and metrics -- and some great resources for investigators.  These resources could include behavioral scientists, chemists/microbiologists, physicists etc.

 - Just a quick note, witchcraft trials happened in Salem, not in Boston. I don't see that as really relevant.

As for places of interest / places of power (pictures of these iconic areas should help illustrate why):

 - Trinity Church and surrounding area out to the John Hancock Tower
 - Bunker Hill Monument
 - The little duck island in Boston Public Garden
 - Faneuil Hall (as a place of interest, not a place of power)

[...] out of time for now, but I hope these notes help.  My thinking of a campaign takes a somewhat different tact from say Baltimore, that there are many small-time practitioners in and around Boston... the White Council doesn't pay Boston much attention because the city doesn't have the pressing worries of a NYC or Chicago... but there's no end of opportunity for trouble to fester quietly while the White Council is distracted elsewhere.  And also plenty of opportunity for scientists, researchers and academicians who don't know what they're doing (or know what they're doing all to well) to get a hold of dangerous knowledge and put it to the wrong sorts of uses.   One funny thing I was thinking of: What happens if the death of the last of a series of curators makes a private library somehow available to the public, and Google Books comes along to power-scan and place on the Internet all these ancient tomes containing information that really shouldn't be made public.  That scenario starts off with no real bad guys, gives the players a serious challenge to try and counter, and the fallout starts the ball rolling on a world o'hurt as it turns out that our PCs didn't plug all the information leaks after all.  Just a thought.