A circular polarizer will often help reflections, but not straight on. While it's a great filter to have, it won't help you here. When I set up to shoot a FTS, even with my standard square tank (non-bow), I typically wait until evening, and turn off all the lights in the room, so that nothing can reflect. It's all about controlling the environment.
Do you have any pictures, just so we can see what sorts of reflections you're talking about?