This is a creative and thoughtful project, especially since Boo is in hiding for most of the book. Here are some ideas:
A blanket: Although Scout didn't realize it at the time, Boo was the one who wrapped her in a blanket when she was outside Miss Maudie's house fire.
Needle and thread: When Jem hangs his pants on the fence when the kids are sneaking around Boo's house, Jem later finds his mended pants, neatly folded "like they were expectin’ [him]" (Chapter 7). Boo found and sewed the pants for Jem.
An image of a window or a window from a Lincoln Logs (or similar) building set: One can only imagine the hours Boo has spent watching Jem, Scout, and Dill from the window of his house. He knows them well enough to know that they are headed for trouble the night of the play.
A mockingbird: Although Tom Robinson is often equated to the mockingbird of this novel (and the reason for its title), a strong case can also be made for Boo Radley. Despite all the rumors at the beginning of the book, the only evidence that the children have of Boo's character shows his kindness and even bravery.
A mirror or glasses: Although Boo ends up being the hero, he still doesn't integrate into society. A mirror (or glasses) could symbolically represent that we need to really see people for who they are and not make dangerous assumptions or believe harmful (and inaccurate) rumors.
The box could be decorated like the fence that separates the Radley/Finch properties. It could also be painted black with stars to represent that final night, when Boo is the hero the kids need.