We have been relying to plugin commander to allow user to enable and disable plugins per blog/ site. However, having the link to your plugins show up under
Dashboard → Posts → Plugins

Is not the most intuitive. Luckily the developers have though of that and make the plug in easy to modify.
Take a look at theline 34 of the plugin-commander.php file. Which should read something like

 define('PC_PLUGINS_HOME','edit.php');

and change it to

define('PC_PLUGINS_HOME','tools.php');

if you want the link to show up under Dashboard → Tools → Plugins
instead or change it to

define('PC_PLUGINS_HOME','options-general.php');

if you want the link to show up under Dashboard → Settings → Plugins.

Here is some WordPress developer documentation, if you would like to know more about the whole process.