Cedar Point is open only on the weekends (except for Millennium Mania - see the offical website for details) in September. Labor Day weekend will be crowded (last holiday before school/beginning of school), though usually not too bad. Other weekends in September should be rather bare, except when Halloweekends begin, which are definately more crowded. Also, beware of limited ride availability (especially on Fridays) because of staffing issues.
Check the official website for dates, Halloweekends, etc.