The box was most definitely one of Regina’s. It had the same logo as Henry Sr.’s grave (SB) and the one on top of the door to the room of hearts (FTL).
Emma has seen those logos, hasn’t she? She could recognize them and/or investigate them and they aren’t hidden so that would prove that Regina was involved. Yikes. That’s like writing a ransom note with “From the desk of [the ransomer’s name]” on it!
Oh, and I also believe those are Snow’s prints from FTL. I’m sure at some point she handled that box. Heck, maybe the poison apple was inside it. Or maybe it was her jewelry box, like someone said. But it would also be easy enough to get MM’s fingerprints in SB and transfer them to the box–that happens in lots of spy shows.