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The long answer depends on how you're playing. On a server or single player, and either casual, survival, or hardcore.
On a server your ship can be stolen from, if you invite a theif into your party.
Here's an unecessary amount of information explaining the safest places to store things for each:
Server + Casual = Character inventory is safest, since you don't drop items on death and your ship can be stolen from if you're not careful.
Server + Survival = No place is really safe. Your ship is probably safest, since you could die and lose your items otherwise. Your ship can't be stolen from while offline, but if you're online it's easier to find your ship inventory than your planet. Also, Planets are the most likely to get corrupted, so it's a toss up.
Server + Hardcore = The only truly safe place while on Hardcore is on a planet. When you die you lose your inventory and your ship, so if you ever want to make another character and get your stuff back you need to store your gear on a planet(specifically a planet you know the coordinates for).
Single Player + Casual = Ship and Character inventory are safest. Planets are still the most likely to get corrupted on single player.
Single Player + Survival = Ship is safest. Planet corruption and dropped items on death make it pretty clear.
Single Player + Hardcore = Planet, same reasons as Server
I have always stored my stuff on planets in single player, it's safer and it means your other single player characters can access it.
I usually have a lot of planet corruption, but from my experience most the planets that have corrupted were ones on which I placed decent sized Colonies. Also, I try to avoid using any crew members on my ship, because they annoy me.
Your experience has been different, but you've noted you have had corruptions due purely to Crew NPC glitches. I may be presuming too much, but it may simply be Colony and Crew NPCs are causing the areas to be corrupted.
So, to package that, the safest storage areas would be either a Planet or a Ship with no NPCs.
Planets are great since you can share between your own characters, but I still prefer ships because I can take the items between single player and servers. As a quick note, there is a ship and a planet file for each ship and planet, so both can be recovered if you make periodic backups of your locations.