I am absolutely in love with Seattle's Pike Place Market. The fact that it is year-round, covered, with regular, official vendors selling everything from fresh flowers to fish, bagels and chocolates, jelly and crafts, daily, at very good prices make Pike Place amazing. Is there anything like that in the Boston area? Or New England in general? I know Boston has Haymarket...but that cannot even be compared...
I don't know Seattle's Pike Place Market, so perhaps my answer will not satisfy you completely. However, Boston has a covered market which is surrounded on both sides by a series of small shops (all-year-round) and lots of stalls, which I presume are there only in the summer. I'm talking about Quincy Market, which is in the area where Faneuil Hall is.
I don't remember whether you have people selling flowers or fish, but surely you have a wide variety of retailers and it is not meant for the tourists only. You can have a look at what is available if you go to Faneuil Hall Marketplace webpage.
I don't think there's anything similar; your best bet might be to try one of the farmers' markets - more details from TimeOut Boston here. These at least have produce and the like, but are only once or twice a week, none year round.
Haymarket / Quincy Market doesn't really compare; apparently Haymarket has remaindered produce, so not comparable with the pick of the crop that you'd find at a real farmers' market; and much of Quincy Market is more like a mall that just happens to be outdoors.
For those not familiar with Seattle's Pike Place Market, it's a year-round market housed in a series of buildings featuring specific areas for fish and seafood, fresh produce, crafts, and so on, and also various storefronts selling books, kitchenware, bric-a-brac and so on, and various food counters. As far as I know, only independent merchants are allowed, so it has a very locals feel - no chains or stores you'd see in a mall. While it's busy with tourists in summer, many locals who live or work nearby in downtown will actually do grocery shopping or have lunch there. There's only a few cities that I know of that have something comparable; Grand Central Market in downtown Los Angeles, Reading Terminal Market in Philadelphia, Granville Island Public Market in Vancouver BC. In other cities, pop-up Farmers' Markets are your best bet.