The easiest way is to take a backup with Backup and Migrate, open it in an editor and search/replace "MyISAM" to "InnoDB". Then restore it.
Personally, I would restore to a new catalog, and then switch the database in settings.php. This way, you can test before making the new version live.
Otherwise, this is a dup of How do I convert a database from MyISAM to InnoDB?
