WordPress is known for being SEO friendly and a multi-site platform is an option for managing multiple sites from one dashboard.
However, you are faced with a bigger issue regarding SEO when it comes to multiple websites.
First and foremost think about your SEO strategy.
Is the content of your top-level domains related to your “master” site or is it different?
Do you want to rank each TLD independently (i.e. geo-targeted content)?
Once you have a clear search engine optimization strategy set you can then move onto evaluating what will work best for multiple sites. One of the advantages that WPMU offers is that you can apply a theme across all sites.
The SEO drawback to WordPress multisite is that the “website manager” does not have complete control of what is published across the “child” sites and this can generate an SEO problem and can be cause for penalization. After all content is king and it weighs heavily on SEO thus having control of the quality of content on the child sites is very important for your SEO strategy.
In short WordPress, multisite can have some SEO advantages but you need to analyze the bigger picture and have a bird’s eye view of your SEO strategy so that you can make the right decision when it comes to SEO for multiple websites.