How can I open these boxes?

These chests are actually impossible to open as 2B.

However, after completing the story the first time and receiving ending A, replaying the game will have you play as 9S. 9S's signature ability to hack machines comes in handy, as he can use this ability to hack locked chests that were unable to be opened while playing as 2B.

During your first playthrough, since you can't do anything with these chests, just make a quick note of where you saw them and move on.

It's worth noting that this ability opens up a lot of previously unavailable side-quests, as well, in case you felt that there was a serious lack of side-quests your first time through.