I recently had to access the ScriptManager in a Master Page from one of the Content Pages.
I first tried to perform a FindControl(), but there's a much easier way.
There is a static method in the ScriptManager class called "GetCurrent()" which provides access to the current instance of the ScriptManager.
//Extend script manager timeout to 10 minutes
ScriptManager.GetCurrent(this).AsyncPostBackTimeout = 600;