Ok so trust me on this, although GSDs are smarter, stronger, and more opportunistic than most dogs, they really aren't as hard to handle as many people make you think they are. As long as you treat your dog fair, train, and just don't let it get away with certain things you'll be just fine. They are herding dogs, and like all herding dogs they like to make sure everything is under control. As long as you keep that control, your dog will fall right in line.
It is just not possible for a 3 month old to challenge anyone for any kind of power. Especially someone that is 10 times its size. Just keep training your dog, make sure the both of you try to train as evenly as possible. My dog was raised between my GF and myself. I am the main handler and yes, my dog listens to me a bit quicker than he does to her, but when he was younger, if she told him to do something, and he didn't, SHE would correct him. I would never step in, or give the command myself. The dog has to learn that it should listen to the both of you.
Try to find a training club where both of you can be involved in the training of the dog. Either training that is available twice a week and so you can do one day and he can do another day, or you do 6 weeks and then your BF does 6 weeks. Make sure that the both of you are constantly training and constantly asking your dog to do things for you. Neither of you should be an "alpha" but both of you should be leaders and yes, higher on the totem pole in your "pack." This is something your dog will learn over the course of the next few months and it is very rare for something that small to challenge one of the handlers and not the other.
I guess my other question would be is if you two live together? If you don't, and your BF just comes over and plays/helps but doesn't stay there, your dog might not have gotten the concept of him being in the "pack." He's just a friend that shows up every once in a while that she gets to play with, and more than likely without a lot of training by him, she'll never really listen to him. My dog only listens to immediate family, ones he sees on a regular basis, and even that is hit or miss depending on how he's feeling. The one thing I can tell you is that GSDs do stop listening to other people and generally will only obey their pack members unless they are regularly trained by random people.