Using PersistenceJS there is a persistence.reset API which will wipe the database clean.
PersistenceJS Site
For developing / testing purposes, you can view content and delete webSQL, IndexedDB, cookies, etc by searching for your domain name at this URL in Chrome:
chrome://settings/cookies
There, you can delete all the storage for a domain or just certain local storage entities. Yes, the URL implies just ‘cookies’, but the interface at this URL includes all types of offline storage.
It would be great I think if the Chrome developer tools interface had the ability to right-click and delete a data storage entity in the Resources tab along with inspecting the content. But for now, all I know of is the settings/cookies URL.