You need to protect your puppy and do everything you can to nurture her confidence. I think you need to sit down with your roommate and come to some sort of agreement, perhaps the dogs should be crated and have free time around the apartment separately until you have their behaviour under control. Your puppy should feel especially safe within her home and with you. If I were in that situation I would consider moving, but I don't fully know the complexity of your situation so that may not be possible for you.
~ Babyawn Bruno Zen (Tchaikovsky) 01/09/2014