Four things to bear in mind
1.The nearer the sub is to you the louder it will sound, you can turn it down and get the same impact. At least site it away form the neighbour's wall, if it fires forwards, then have this pointing across the room, so the neighbour doesn't get any direct bass. Try moving the room around.
2. Moving air is all that matters, if you sub is sat directly on floorboards, then it will be making them vibrate also; this vibrates through to next-door. Try sitting the sub on spikes on a concrete slab; the spikes will reduce the amount of direct vibration to the floor and the slab should soak some of the remainder up.
3. A sub sat in a corner will boom and make the walls vibrate, which goes to next-door. Put it in free as space as feasible.
4. After all this the real problem is that your neighbour is complaining let her know that you are taking this seriously and have done something to help, if she is expecting less annoyance then she may accept the result.