Some searching around in the registry suggests that under 32-bit windows there should be the following key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\NET Framework Chart Setup\NDP\v3.5\Version
On 64-bit Windows there is an equivalent key here:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\NET Framework Chart Setup\NDP\v3.5\Version
On several systems (with .net 3.5 SP1 and chart controls installed) that value reads 3.5.30730.0 so that seems like a reasonable place to start.