There are numerous places in the Boston area to buy whiskey, but I'll just list here the ones I like to use. If you find something else that suits you better, go nuts! I'll also list the people at each of these locations with whom you should speak if you stop in.
Atlas Liquors (3 locations: Medford, Quincy, and Roslindale)
Speak with Jeff Fine, the owner and resident whiskey aficionado
Federal Wine and Spirits (29 State Street, downtown Boston)
Talk to Joe Howell, their extraordinarily knowledgeable whiskey guy
Julio's Liquors (Westborough, MA)
Check in with Ryan Maloney, the owner and whiskey guy
New Hampshire Liquor Stores (Um, all over New Hampshire)
You can conveniently check their inventory and prices online to use as a benchmark for other retailers' prices
If you can't find something you're looking for at one of these locations, it's probably not for sale within hundreds of miles.