For a physical location:
* Port: This is the most common and direct synonym.
* Docking: This refers specifically to the act of bringing a ship into a harbor.
* Marina: This refers to a harbor specifically for pleasure craft.
* Haven: This implies a place of safety or refuge.
* Bay: A large body of water partially enclosed by land.
For a feeling or action:
* Shelter: To protect or provide safety.
* Conceal: To hide or keep secret.
* Nurture: To care for and protect something.
* Foster: To encourage or promote something.
* Entertain: To allow a feeling or thought to stay in your mind.
For a metaphorical sense:
* Hold: To keep or possess something.
* Nurture: To encourage or support something.
* Embrace: To accept or welcome something.
The best synonym will depend on the specific context in which you are using the word "harbor".