The /etc/my.cnf file is a simple text file on your VPS that you can edit. Do a text search for the variable you want to change. However, before you do that, I would optimize Wordpress first, which will decrease the load on the server and MySQL and may make altering your MySQL server variables moot.
Have a look at the Codex article on optimizing Wordpress.
You may only need to add a caching plugin like WP Super Cache configured with mod_rewrite and switch wp-cron to an actual cron job to make a big difference.