Is there anywhere that has fresh mitarashi dango?
Someone in the area must make it, since the late Yoshinoya in Central Square used to carry it. (I'm not sure that the Kotobukiya even did...) Unfortunately, with these both closed, it's kind of low moment for finding Japanese items in the area, but that also means that the list of places to try calling is conveniently short: you could try Cherry Market on Newbury, or the new place in Brookline Village.
Do you mean fresh as in freshly made, or just not-frozen? The only place I'd ever seen them was at Kotobukiya, but they were pre-packaged and sat in the fridge section. Not sure how fresh they are. I haven't seen them elsewhere, though I haven't been to the new market in Brookline Village yet.