Docker daemon runs in a separate VM, so in order to clear logs you should do the following steps:
First, you can find the log path inside the VM, with:
docker inspect --format='{{.LogPath}}' NAME|ID
You can connect to the VM with screen
screen ~/Library/Containers/com.docker.docker/Data/com.docker.driver.amd64-linux/tty
Here you can simply use output redirection to clear the log
rm -Rf /var/lib/docker/containers/CONTAINER_ID/CONTAINER_ID-json.log
And finally you can detach the screen with hitting Control + a d