Back on Topic: I don't know of many safe boxes outside but you can use http://fallout.wikia.com/wiki/Harper%27s_shack and once you've completed Dead Money you can use the http://fallout.wikia.com/wiki/Abandoned_BoS_Bunker.

- You could test the boxes yourself, put something worthless to you like ashtrays or tin cans in boxes and wait 3 days, then return and if it's still there you can assume it's safe. You might want to put a weapon in as well incase only weapons get taken- a 9mm pistol would do.

-- Now that I think of it, the shack just before the Boomers has a suit case and a box next to the truck, you could use that if you wanted since no NPCs are there once you kill the guy offering help to reach the Boomers.