I want to simulate the traffic flow of the existing commuter trains and proposed monorail system in city within the other modes of transportation (Street Network).
You can use Arena Simulation software to simulate technological processes . Please see in my profile - there are a papers when is used Arena simulation Tools for simulate train movements and the interval in metro, and also technological processes in metro stations.
AnyLogic railroad library could be the solution. But you should have basic JAVA programming skills, as the complex logic should be described in code. Read more here https://www.anylogic.com/rail-logistics/
I have made good experience with VISSIM and OpenTrack http://www.opentrack.ch/. However, since you seem to look for a macro or mesoscopic simulation VISSIM might be preferable.