Backup your Database and then use DROP statements to delete the tables manually via tools such as MySQL Workbench, or MySQL Query Bench. There are many alternatives you can use that provide GUIs for backuping up, restoring, and modifying DBs.
Here’s the WordPress DB schema, do not delete any of these tables:
http://codex.wordpress.org/Database_Description
Aside from that, those tables should have no impact on your site at the moment, so long as the plugins are disabled there should be no slowdown
TLDR: Backup DB, delete things, see what breaks, restore if broken