A quick look at the map reveals 2 perfect things about Boston:
First, it is directly at the ocean. A lot of Lovecraft's monsters live in or come out of the ocean, which makes Boston an ideal place for something lovecraftian from the get go.
Secondly: There is a place called "World's End" right there in the bay. Admittedly, it is not exactly in Boston, but neither was Victor Sell's Lakehouse. A hidden tunnelsystem leading to a cave, where some cult is trying to call up the OLD ONE. On that note, the OLD ONE could even lie beneath that very island. Yes, it's been done, but that doesn't mean it can't work.
Honestly, Google Maps and Google Streetview are great tools to get started. If you find something interesting, even if it is only by name, pick it out and you will soon have more ideas than you can carry.