We don't know, but probably someone under the instructions of Sister Grace.
We do know from the episode that the body was discovered by a man called Walter Rafferty. Every year, he revisited the spot where he found the body. We also find out that he's not the only visitor. Every year, a woman in a green coat brings a rose to the location.
As the episode progresses, we learn that this woman is Sister Grace. We also learn that Sister Grace is the mother of Arnold (the boy in the box), conceived with a man called Clayton. Arnold instinctively seemed to know this, as he wanted to remain with the sisters as opposed to getting adopted.
Despite this, Sister Grace is eager for him to move on. She is concerned about his behaviour and basically convinces Clayton to give him one of the treatments being done in his work. These treatments are radiation related and should not be used on Arnold. Sister Grace, however, is hopeful they will work. Alas, they do not - Arnold dies soon after and the Sisters put the body in the box.
So we know this then:
- Sister Grace was really Arnold's mother.
- Sister Grace desperately wanted Arnold to be adopted, inadvertantly causing his death through the radiation treatment.
- Sister Grace visited the place his body was found every year.
This strongly suggests that the suitcase given to the police, shortly after her death, notifying them about the case, was related to her. Whether her will stipulated it be delivered, or a friend did it, we don't know. It just seems very likely she is the root cause of it.
Ultimately though, the mystery works in this episode. The Boy in the Box is based on a real life, unsolved murder. Whilst they effectively discover what happened in this episode, who alerted them remains a mystery. This ties in well with the fact that the case's real life counterpart is unsolved and thus a mystery as well.