Assuming Tomcat is running as an actual Windows service, it helps to know the executable the service uses
It is often Tomcat7w.exe (or a different number for a different version of Tomcat) so check the service configuration for the executable, you would see something like:
C:\Program Files\Apache Software Foundation\Tomcat 7.0\bin\Tomcat7.exe" //RS//Tomcat7
If you double-click on the Tomcat7w.exe, it will open up a window and if you click on the Java tab, you can add the Introscope parameters for the agent in the Java Options window.
There is more information below on configuring the Windows service, this can be useful where the Tomcat service name is not the default one.
https://tomcat.apache.org/tomcat-7.0-doc/windows-service-howto.html
If a different executable is being used, the Java configuration could be configured elsewhere, like in a wrapper configuration or even Windows registry.