Boston
I'll suggest doing a search of the Boston Board for "neighborhood" and posted by "impposter". You'll get many of the previous threads with lots of advice and descriptions of the different places to see and stay in Boston and the 'burbs. I also post a Boston neighborhood map, such as the one below.
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To help the out of towners, Copley Square is a smaller area within the Back Bay neighborhood on the map below. Maybe near the "K" in bacK bay.
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I'm a local guy, so I think that getting around downtown Boston is easy peasy. It is VERY walkable and there is also "the T" (the T is Boston's MBTA Subway System). Guys who live or work in Boston would have no problem getting from the Financial District to the Waterfront (alert! there are TWO "waterfront" neighborhoods! Make sure you're talking with others about the same one!) to Copley to Fenway.
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Some of those prior threads will also mention the idea of spending some of your trip in downtown Boston (maybe Copley Square) and some of your trip in the 'burbs. Waltham is popular because it is the intersection of the east-west Mass Pike (I90) and the north-south Route 128 / I95 "belt". It is easy for the E-W (inbound - outbound) commuters to make a quick stop and for the N-S ('burb to 'burb) commuters, too.
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Years ago, some of the suburban hotels (e.g., Waltham) offered shuttle buses to Logan Airport maybe with a stop in Boston. I have no idea if any of the hotels still offer shuttle services. If you call for rates or reservations, ask about shuttle services to/from Boston. Uber is surely available but there might be private shuttle buses (like those mini 12-person buses) with service from the hotels to downtown.
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Here are some older posts:
http://www.theeroticreview.com/discussion-boards/boston-9/walkable-and-shoppable-224034
http://www.theeroticreview.com/discussion-boards/boston-9/a-few-qs-and-then-suggestions--and-a-boston-neighborhood-map-226278
http://www.theeroticreview.com/discussion-boards/boston-9/intown-vs-suburbs-neighborhood-map-222475
http://www.theeroticreview.com/discussion-boards/boston-9/back-bay-and-seaport-are-both-good-options-222497
http://www.theeroticreview.com/discussion-boards/boston-9/boston-neighborhood-map-convention-center-two-waterfronts-219728
http://www.theeroticreview.com/discussion-boards/boston-9/boston-neighborhood-map-221455
http://www.theeroticreview.com/discussion-boards/boston-9/re-logan-airport-is-a-favorite-of-some-gals-220039
The best deal in terms of cost is at the airport, and north of the airport on Route 1A. These are also sort of convenient to get to. The down side is that there is nothing to do there except watch airplanes come and go. The most convenient are the Copley Square hotels because they are very easy to get to right off the Mass Pike (I-90), and there is a ton to see and do around there. But the cost is very high. The downtown hotels aren't too expensive, and there's a lot to do around there as well, but very inconvenient to get to.
The suburbs are an economical choice, but again, not much to see and do.
The best deal in terms of cost is at the airport, and north of the airport on Route 1A. These are also sort of convenient to get to. The down side is that there is nothing to do there except watch airplanes come and go.