Your son needs op to execute adminstrator commands on his playerserver. To ensure this, go to the web panel and head to the console:
Proceed to type "op [username]". Replace [username] with your son's username.
After they're op, try executing /weather clear. Alternatively, you can execute /weather clear from the console itself. This should fix the issue.
If the issue still persists, it is likely there is a Repeat Command Block that sets the weather to rain. If so, disable command blocks from the Settings tab.