some subdomain pages have better ranking than the main domain

So my company has an old website: **xxx\[dot\]com**. Then they want to create a new one, so they opened a new server and created the new website **www\[dot\]xxx\[dot\]com**, but they did not put it live in the first place. Then they created the subdomain **sub\[dot\]xxx\[dot\]com (for other customers)** from the old website, and they made the subdomain live for a while. For few months later, they put all the 301 redirects from the old website to the new website and made it live. Also, the subdomain and new website have 90% of the content similarity. In the subdomain, I put the canonical tag and point to our new website. I was thinking of putting all the noindex tags on the subdomain, but I am afraid it might hurt the new website as well... The problem is, that some keywords on SERP, show the subdomain, not the new website. Also for certain keywords, it shows inconsistent results between the subdomain and the new website( e.g today shows the page of the new website, and it shows the page of the subdomain the other day)... And they don't want to differentiate the content between the subdomain and the new website....so I have no idea what to do now.