CS is more general, but will give you the skills to build software. System Science is a less common major, but its focus is closer to what you're looking at, I think: modeling complex systems as software, and learning things from emergent interactions.
A lot will depend, of course, on what you're trying to model. A flight simulator cares about how a plane reacts to a pilot, and how the plane interacts with the air (and, occasionally, the ground). This is a detailed simulation with a few very complicated parts.
On the other hand, an agent-based simulation of a bunch of pedestrians walking through a crowded space doesn't consider the aerodynamic forces on each person. That's not relevant. The interesting bit there is to create a simulation that accurately captures how people behave in crowds, and use that to test interventions that affect crowd behavior.
A team building a flight simulator is going to need some mechanical engineers, aeronautical engineers, and someone familiar with 3D computer graphics (this person probably has a CS degree). A team working on a crowd dynamics simulation is more likely to have psychologists, anthropologists, and someone familiar with agent-based simulation (this one has at least taken some system science classes, if it wasn't their major).
Honestly, consider going to one of the military schools (west point, annapolis).
Plan "B" could be computer engineering. Check with the schools to review the diversity of the computer courses within the college.
For example, Rowan University has an electrical and computer engineering program. When my son was looking, there were less than a dozen schools with this 'computer option'.