Where do you live near, and what times do this happen?
I doubt it is any trains. The Acela is a lightweight body consist. If there were any train "concussion" it would only be from crossovers (switches) and those can be found at Forest Hills and again between Green and Stoney Brook. However, while the switches at Forest Hills are noisy when some trains go over them at a high speed, if they were shaking a nearby home I'd expect they would be coming off the track. The Acela is the lightest and least-noisy of any of the trains running on the Northeast Corridor.
I live in Roslindale very close to the train tracks and while I hear them, there is rarely any vibration from them, at least any of concern. However, I grew up next to these tracks so some vibration is normal for me and I can easily sleep through it.
Now, along this same topic, I have occasionally felt some kind of earthen concussion not far from Roslindale Sq. where I live. It sounds and feels like someone closing a door in an apartment underneath me, though no one is home. It may also feel like a truck bay door closing out on the street when no truck can be seen within sight. It is a distant feeling.
New England is prone to an occasional Cat 1 to Cat 3 earthquake as you may know, and it was not that many months back that an earthquake in Virginia was telegraphed through the earth's bedrock all the way to Boston, forcing evacuations downtown and at Umass's campus.
Alternately, it is the Morloks tunneling under us - of course I jest, but that is my nature.
So unless you have dishes rattling or falling off the shelf, I'd not read much into it.
Alternately, you can always call the Weston Observatory (NOAA) where the local quake readings are taken to see if they are registering anything in the area.