You need to find a safe container. If you have completed "The Power of the Atom" quest you should have a place to live, either Megaton or Tenpenny Tower. Both of these have multiple storage containers. Alternately, if you want the fastest access without 2 or 3 loading screens, use the blue mail drop-off box in Springvale. It is the one immediatly on your left as you head into the town from Vault 101. No one ever goes past this box to steal anything from you, I have kept tens of thousands of caps woth of loot in there and it never goes missing. If any NPC comes across a better weapon or armor than they have, they will take it, so many outdoor lacations should not be used as someone might take your stuff. Almost all interior not owned by the environments 'reset' after about 3 game days, deleting your gear.