General:
* Sanctuary
* Refuge
* Safe haven
* Retreat
* Shelter
* Asylum
* Harbor
* Safeguard
* Bastion
* Citadel
More specific:
* For animals: Lair, den, burrow
* For people: Home, abode, dwelling, retreat, hideaway, getaway, sanctuary, asylum, refuge
* For ships: Port, harbor, anchorage
The best synonym will depend on the specific context in which you are using the word.