I lived in an apartment for a few years with a couple side-firing cube-type subs. The flooring was hardwood over joists covered in carpet. Beyond the usual acoustic energy being transferred via the air to walls, floor and ceiling, there was a good deal of vibration from the cube directly transferred to the flooring. I ended up raising the subs about three inches off the floor on vibration damping materials. Not that my feet are calibrated instruments, but I could tell a small difference. With the damping materials in place the floor seemed to transfer no more or less energy than the walls did. So my vote goes to something like the Gramma mentioned by gonk as your best bet in making at least a small dent in the energy transferred to the flooring, regardless which direction the sub ‘fires’. The walls? That's another story.

Is your flooring wood on wood joists, cement with rebar on steel I-beams, with/without carpet, or…? If wood-on-wood or another option without as much mass as cement, you could also try changing the resonance of the floor near the sub with the addition of a good deal of weight (mass) on the floor.