At the beginning of Chapter 7, Scout asks Jem about what happened the night he went back to the Radley's yard to get is pants. He says, "They’d been sewed up. Not like a lady sewed ‘em, like somethin’ I’d try to do. All crooked." When they find the ball of twine in the knothole, Scout thinks it is another child's hiding spot. However, Jem thinks otherwise. He doesn't specify what he means by this but the indication is that, if it is not a hiding spot, the twine was put there to be found (by he and Scout).
When they find the soap dolls, Jem and Scout rule out Mr. Avery and Miss Stephanie's sweetheart. After finding the pants sewn together and now these surprises in the tree, the reader can suppose that Jem might think it is Boo Radley who is behind these gifts. Jem never says this aloud or to Scout. And there is no direct textual evidence to absolutely prove that Jem thinks this. But there are hints. The fact that he never tells Scout what he's thinking or who he thinks is responsible is important.
He had been on the verge of telling me something all evening; his face would brighten and he would lean toward me, then he would change his mind. He changed it again. “Oh, nothin‘.”
Scout, on the other hand, seems to have no clue that Boo is the one putting things in the tree. When they start to write the letter to thank the mystery giver, Jem says it should begin "Dear Mister." Scout asks why he assumes it is a man.