An unusual problem

Turn your subwoofer off after 10pm. Headphones is another suggestion. This is one of the drawbacks of apartment living. On the flip side,I’m sure they’ll create noise that will disturb you as well. It just one of the many compromises in life.

    I suppose you could also try a “subdude “ subwoofer platform. I’m just not sure how well this would work in your situation. Lower frequencies just seem to travel everywhere.

Acoustic panel to absorb the bass at the windows or some means of damping the glass? 

It may help if the sub was right next to your seat. In phase and lower volume. Or headphones. 

Dynamat products are used to dampen the inside of car doors to quiet the inside of your car, improving the sound of car audio.  This may work well to dampen the glass vibrations.  

There are also quilted blankets, woven with batting available, much like the packing blankets Penske trucks issues.  These can be found with metal grommets so one can suspend them on the wall with small nails.  They can weigh 9lbs. each.