Neither is better. The difference is that "into" conveys a direction of motion (into the box) whereas "in" only conveys position (inside the box). Your choice depends which of these ideas you wish to express.
It is similar to the difference between "to" and "towards". Consider, for example, the sentences:
"Jack threw the ball to Bill"
"Jack threw the ball towards Bill".
The first only indicates the ball's destination. The second indicates the direction of motion, not explicitly stating that Bill is the intended recipient.