I know what you mean, it seems like every non-official house is too unlivable because of enemies, ugly corpses lying around, or lack of decent storage.
One good place I'd reccomend is the bunk room in Farragut West Metro Station. None of the enemies there respawn, there's no skeletons or icky mutilated corpses hanging from the ceiling, and it has some good storage spots and shelves to use. There's even a computer terminal on the desk that can lock and unlock a nearby safe to store your gear.
Me personally I perfer the Tenpenny Tower Suite just because it feels like a real comfy place to live and it's really safe from the hellish wasteland.