So, welcome to the police world, and mounting weapons. How's this for an idea: THE LOFT (Electronics Tray) | Weapon Storage | Trunk Storage | Products | Lund Industries

Nothing vehicle specific to a 4runner, but a very nice way to tuck it up overhead and locked.
There are other mounts used to mount weapons to the trunk lids. If you do a little searching for police weapon interior mount, you'll find some awesome stuff. It's not the cheapest, but it's made so that no one can get it but you. In fact, there's quite a few cool options with power locks, too.

If I was setting up a 4Runner for one of my unmarked units, that's the direction I'd look. It's usually preferred to be a second lock after the vehicle lock, so an electronic lock mount on the hatch might work?

Oh, the fun of weapon mounting!