I've some experience with the University of Virginia so I can help shed some light on this.
Computer Science is programming. AI, compilers, memory management, security, operating systems, etc. If it's part of software, it falls under CS.
Computer Engineering is a mix of CS and more traditional Electrical Engineering. It deals with computer hardware as well as the software that interfaces with it (i.e. firmware). CE at UVA is that Venn Diagram overlap between CS and EE. It covers everything from chip design to Operating Systems.
Systems Engineering is sort of a higher level overview of engineering principals. I'm the least familiar with this one. It deals with things like product life cycles, risk management, and the work process. Looking at the list of Systems concentrations might give you a better feel for it. UVA has one of the few Systems Engineering undergrad programs. Most people who do Systems major in a more normal engineering program in undergrad before pursuing a Masters in Systems.
To get a better idea of the programs, you should check out the grad level classes you would be taking in each. For this, you want to use the unofficial class listing site called Lou's List. All three departments are part of the Engineering Department. Gradate classes will be those numbered 5000 or higher. Look at listing for both this coming semester and previous semesters.