Low frequency sound is composed of fairly long wavelength pressure waves and can cause noticeable physical vibrations which will also produce the same sound. Your problem is likely that the subwoofer is shaking the floor itself directly which turns your neighbor's ceiling in to a speaker.
If this is the case, your best bet is to provide physical dampening between the floor and your subwoofer so that it can not directly shake the floor. If you can elevate it that would be ideal, but if not, placing soft vibration absorbent materials (like towels, or better yet, thick flexible rubber as frcake suggested) or something similar below it to isolate it from the ground is likely to help considerably.
I was finally able to take a look at a picture of the sub and see it's already reducing it's contact area to four relatively small legs. This means the towel idea is going to be much less effective than rubber stoppers (the more concentrated weight will allow more energy transfer to get through while the rubber stoppers will allow side to side movement) and that it's likely a good portion of the energy is already going through due to air pressure hitting the floor rather than direct rigid transfer. If that's the case, then the dampening may not help that much, but it should still do something.