Javascript is processed linearly, so the more data is loaded, the longer it takes. I would suggest the type of load on demand, showing only part of the data at any given time.
Otherwise, I would suggest switching to Flash / Silverlight (if you are developing .NET)
Edit
Visifire Silverlight. http://visifire.com/.
, MS MS (http://code.msdn.microsoft.com/mschart), .NET FrameWork 3.5 SP1, WinForms/ASP.NET( , ASP.NET AJAX ).
FusionCharts Flash: http://www.fusioncharts.com/free/