Basically, these are two PowerShell modules.
MSOnline : The MSOnline Module contains -MSOL cmdlets, was the first version of Windows PowerShell which refers to version 1.0. It is the old module which provide some functionality which are not available in AzureAD module.
Azure AD : Microsoft refers this module as a newer version i.e 2.0. The Azure AD module, and its dependencies can be installed from PowerShellGet from PowerShell gallery.
Nowadays, Microsoft refers to use Azure AD.
I hope this will clear.
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