Similar meaning, but more neutral:
* Chuckled
* Giggled
* Laughed quietly
* Smiled faintly
More negative connotations:
* Sneered
* Scoffed
* Jeered
* Mocked
* Laughed at
More playful connotations:
* Tittered
* Whispered
* Murmured
The best synonym will depend on the context of the sentence and the intended meaning.