There are tons of good subs - I would recommend you review the posts and sub reviews and simply pick a good sub. Don't pick one to compliment very poor speakers, pick on to compliment very GOOD speakers, then work towards getting those speakers. SVS, Velodyne, etc. There are a bunch of good sub companies.
Set your speakers to small - even then they will have issues unfortunately. The Bose cubes aren't designed to handle a good bit of the mid-range so that will always be gone until you get new speakers. This fact you will have to live with for the time being.