I would like to know which degree out of these two would better prepare me for Information Systems Security. I want to eventually work with the CIA as a Information Systems security specialist however I've already put two years of work into my CIS degree and was wondering if i should transition over to the CS side. If not these two degrees, then which degree would best prepare me to reach my goal. What should i primarily know to be proficient in computer security field? Would a CIS degree and self teachings be enough?
CS would definitely be more useful as far as starting a career in general is concerned, but even if you went with Comp Sci you'd still have to either learn on your own, through your career, or through a degree/cert program a good bit of the security related aspects as most schools don't focus heavily at all on it.
(That's not to say CIS wouldn't work at all for your career goals, but it really depends on what you'd like your focus to be)
Does your current university have an ISS degree program? I know a lot do not, but some do so if that is what you had your heart set on you could always do that.
It depends on what you'd want to do in the security field what you'd need to be proficient in. Crypto would require a stronger math (and depending on what you were doing, software engineering or at the very least programming) background than say...application hardening.
If I were you and I had my heart set on ISS but my school didn't have the program I'd go with CS, learn everything I could, and see from there what interested me most. I'd then start a job in it if I could, if not I'd start a job doing something similar that I would enjoy and learn there and on my own.
Good luck regardless