Of course one quick way to do it is to go to Safari's Preferences > Privacy > Manage Website Data..., find the website you want to delete IndexedDB storage for and delete. Unfortunately this will also remove any local storage and cookies, not always what you want when programming.
That will delete just the database you are after, a nice and clean way of doing it.
There is one more way to do it, and that is to open Finder, the click on the Go > Go to Folder... menu item and enter "~/Library". From here you can look for Safari > Databases > __IndexedDB and delete any databases you don't want.