How about the Quincy Marriott? They have a shuttle to the Red Line
One end of the red line ends in Cambridge. At that Cambridge Alewife station (end of the line), the Best Western Hotel Tria is walking distance and a bit less expensive than centrally located Cambridge hotels (but not always)
Quincy is the bargain area on the red line. Look at the Quincy Marriott (often featured on LastMinuteTravel.com as a hidden hotel), and the Best Western Adams Inn. The Marriott has a shuttle to the T. Not sure whether the Adams is walkable or needs a shuttle.
Your question is very specific, but are you really looking for hotels with convenient T access to Harvard Square? They don't necessarily need to be on the red line. A train change is easy and there are more hotel options on the green line.
Is your goal to find a less expensive hotel? If not, then all centrally located Boston hotels have easy access to Harvard Square.
Feel free to ask a more specific question and includ dates and budget. You may get lots of helpful suggestions.
I think that the first reply to your post has it correct with suggesting the
Boston Marriott Quincy
A second choice to consider
would be the Holiday Inn Express Braintree
You should allow about 40 minutes into Harvard Square, and you could check the MBTA website for maps and the trip planner in the rider tools
There's also the Courtyard Marriott in South Boston and the Holiday Inn Express on Boston St. in South Boston, both are near Andrew Station on the Red Line.
I go for the Quincy Marriott .
I think other suggestions are good, but I will add one comment that's outside the box, i.e. red line.
There are many bus routes that go into Harvard Square. This should expand your search area.
This place near Davis Square sounds nice:
it would be very convenient to the Red Line.
I wouldn't call Quincy a "Bargain" area, since that word has negative connotations. The Marriott is good and the Adams Inn is a hidden gem with waterfront views on the Neponset River. It's walkable to North Quincy, but it's a longish walk. Lots of restaurants nearby. I wouldn't recommend Quincy for going to Harvard because of the distance. Dorchester/Southie is closer, as stated above. It just seems like a hike if you have to be in Harvard Square.
The OP is almost a year old.