Individual site If you have a site with slug blog on a WordPress multisite instance using subdomains, you can use the full URL to run a command against the site:
wp --url=blog.example.com
Think of the --url= parameter as any URL you can put in your browser.
Multiple sites Need to run a given WP-CLI command against multiple sites on a WordPress multisite install? You can do so using a combination of wp site list and xargs.