Paddle Boat
You need to get one of the paddle boats that tourists use in the Inner Harbor. Then you could ride from home to your boat, paddle across the harbor (with your bike on the back) and then ride the rest of the way to school. Of course, finding places to dock the paddle boat will not be easy and paddling a little dinky boat across the shipping channel in Baltimore Harbor may not be the smartest idea in the world. But, you asked for suggestions.
I know generally where you live and if you are taking the Harbor Tunnel, you must be going to Anne Arundel County. There is no way to avoid the Tunnel without your going through Downtown and neighborhoods that are a lot worse than my usual commuting places. I also don't think that there is any bus link that would get you and your bike through the Harbor Tunnel -- all of the mass transit connections between the northern parts of Baltimore and Anne Arundel County go through Downtown. You could take your bike with you in the car and ride from the southern end of the tunnel to school, but the riding in Northern Anne Arundel County sucks. If I were you, I would just get out of school as early as I could in the afternoon, get home and then jump on the bike and ride near your house, which is a lot letter place.