little, soft | deep/deep-throated, low

give, have, let out
She gave a little chuckle.

suppress | hear

with a ~
‘I was only kidding,’ he said with a low chuckle.

~ about/over
We had a chuckle about it afterwards.

softly

about/over
She was still chuckling about the story the next day.

at
He chuckled at the thought of the two of them stuck in the snow.

chuckle to yourself
She chuckled softly to herself as she remembered his astonished look.