Here's a list of factions that will matter.
Mortal
The Mob
Its really two groups of ethnic mafias that I will expand on as needed. In the north part of Boston its the Italians and in the south part its the Irish. Both are dangerous and powerful though they compete with each other so their total influence is lessened across the city and limited to their own neighborhoods.
The Police
I include the FBI here. Law enforcement is trying to crack down on organized crime but its difficult due to the local police being incredibly corrupt as well as heavily infiltrated by the mafias.
Supernatural
The Vampire Courts
All the courts are represented in Greater Boston: Red and White, and even Black and Jade.
The White Court holds sway in the cities and suburbs directly north of Boston as well as those of the South Shore of the bay (Cambridge, Medford, Revere and all the way to Lynn in the north, Weymouth, Hingham, Cohasset, Hull and Scituate to the southeast).
House Raith is based in Hingham among the debutantes and urban elites who prefer the seaside access and relative quiet of the town. House Skavis is closest to the city center in Cambridge where they can prey upon students of the elite universities who are overwhelmed by their work. House Malvora is further northwest in picturesque Lexington where they claim they drove the Colonials so mad with fear that they rebelled against mighty Britain.
The Red Court is entrenched to the west in Framingham and in conflict with the Jade as it tries to expand into the city center. There is a smaller pack out of Providence, RI that is expanding north as well.
The Black Court is only a few individuals based in Salem. They are very interested in crushing the White Court but since their weaknesses are so well know they cannot act openly.
The Jade Court is ensconced in Chinatown, the western neighborhoods of Roslindale and Jamaica Plain as well as the city of Quincy which has the highest population of East Asian immigrants in the state.
The Faerie Courts
There is almost no presence of the Winter and Summer Courts in the Boston area. They are the only ones who know that there are dragons in the area and they want no part of that.
There are plenty of Wyldfae, but they are scattered across the region and only congregate in small numbers of similar fae.
Changelings are quite common as well with perhaps 1000 total among the total population of 4 million.
The Formor
As a major port it is no surprise that the Fomor are present and active. They are ruthless and wicked though so they tend to compete with all other factions, but since there are so few of the Winter and Summer fae to oppose them their strength has become dangerous.
The Outsiders
Its no coincidence that HP Lovecraft set most of his stories in this area. There are many cults who foolishly seek the attention and favor of the Old Ones, particularly The Sleeper, The Hydra, He Who Dwells in the Deep, and The Goat With A Thousand Young.
They are allied with the Fomor in so far as they have similar interests in the Outsiders and in the degradation of themselves and their victims.
The White Council
Wizards are everywhere mortals are and they band together because they know supernatural creatures are incredibly dangerous. The Council in Boston is centered in Cambridge around the vaunted campus of Harvard University.
Given that they are centered in this, the oldest university in the United States, they maintain many of the old traditions. Of these the most obvious is that female wizards are generally excluded from the male-dominated circles of the Harvard Council and have their own group known as the Radcliffe Witches.
Despite the best efforts of the old boys club the Ladies of Radcliffe are an influential block with near parity of total numbers. This actually makes them the largest faction since the men have several different societies dating back to the foundation of the college in the colonial era.
Werecreatures
Not exactly an organized faction but by being similar many of them tend to congregate together.
Werewolves tend to live in or near the heavy woods to the west and north where they can run free without freaking the mundanes. So they hardly matter.
Werecats and werecrows on the other hand are well represented as well as a cast of werehawks who very much do not get along well with the former two and the feelings are mutual.