We hear a constant bass subwoofer like thumping noise every night from about midnight to 7 am
Listen, sound patterns travel in the weirdest ways.  My house is on a hill and there is a college a block away.  Every night my house was shaking from bass and I was like "what the hell".  I am thinking the kids were cranking up their bass so I ventured out on a recon mission.  

After a few nights of visiting the parking lot area I did realize it was a few kids.  But their music was kind of loud but really not bad at all.  The sound waves just climbed right up the hill and bam hit my house.  I just asked them to move literally 30 feet over behind a tree and have never heard them since (and they still hang out there).

For your issue you have to get rid of all of your power for a night to make sure its not you.  I believe you when you say its your neighbor but check yourself first.  I did have a roommate in college that slept with semiloud music on all the time. 

As for traveling through pipes... I doubt it.  Unless their system is setup right next to the sewar lines or main stack really there is no way.  Most bass back echos.  So if they have a system that is facing away from your house in their room facing you, that would make more sense.  

I would talk to the neighbor.  Your options for making this sound go away on your own probably involve a tree or fence which I am not even sure is possible.