I've forgotten what they call it... the Liberty Walk? Basically it's a walking tour of the city by a tourguide in Revolutionary period garb. That's kinda cool because about half of it is schlepping through cemeteries.
Another alternative is that you are basically a 30 minute train ride from Salem, which is basically Arkham (only with more dragonsblood incense). Naturally, the town has capitalized on the witchcraft/witch trials thing, but some of the museums are pretty cool. And, even if you've only got a couple hours, you can totally get some good sights in, hit a couple museums, get some chow and have time to duck into Harrison's Comics on Essex St. on the way back to the train station. Yes, from the depot you can walk to everything cool in Salem in short order.
Of all the places I checked out in Salem, the BEST was a wax museum dedicated to classic horror called "Count Orlok's Nightmare Gallery."
There isn't much particularly Lovecraftian in Boston (IMHO, others' mileage may vary), other than obscure things like trying to find Pickman's address. Otherwise it's just a beautiful city (though not as well laid out as Chicago), full of women in skirt-suits, smoking, talking in loud Colin Quinn voices and dropping f-bombs every 3rd word. HPL probably wouldn't approve