Multisites with multicron
To analyze the performance of each multisite you will need to coorelate web server logs with performance logs or use an APM service like Newrelic where you can watch PHP at a very granular level as the cron jobs run.

Unfortunately, there is no easy fix for your problem. Multisites can only be used when the sites are not complex or demand a lot of processing. I believe you have a decision to make. 


Keep using the multisite function of Drupal and deal with the performance issues you have in complicated and creative ways. Create ways would be using multiple servers and databases to offload the cron jobs to so it does not impact the websites.


OR


Break the sites up into different Drupal installations and use a code repository to manage the multiple sites. 


You should read the articles written by Pantheon on Multisites. They had the same problem as you and realized the problems (performance) with multisites and devised another way to run complex multisites.