How to set internal autoreply:
Set-MailboxAutoReplyConfiguration -Identity emailaddress -AutoReplyState Scheduled -StartTime “mm/dd/yyyy hh:mm:ss” -EndTime “mm/dd/yyyy hh:mm:ss” -InternalMessage “message

How to set external autoreply:
Set-MailboxAutoReplyConfiguration -Identity emailaddress -AutoReplyState Scheduled -StartTime “mm/dd/yyyy hh:mm:ss” -EndTime “mm/dd/yyyy hh:mm:ss” -ExternalMessage “message” -ExternalAudience All