Where did she get John's eye?

It was presumably along with his service weapon in the box of possessions Lamar provided her.

Of course all of that beggars common sense. The eye would have deteriorated beyond recognition by then like any piece of unpreserved flesh. Furthermore, it's absurd to imagine that it would have been included amongst John's possessions in the first place, but very little in the movie makes sense.

I think you have to few it as a satire on the lengths society is willing to go to indulge the illusion of safety.

John obviously put it back in the bag and put it in his pocket and then either gave it to her or took it out of his pocket and left it when he was at their house before the cops came to get them. They just of course didn't show us that part. And yeah it should have been decrepited by then but since he wanted to keep them, the doctor probably put some kind of preservative solution on them. Maybe formaldehyde or something.

He came to her house with the precog. He probably gave it to her then.