It really isn't fair to compare CSI's nursing program with Hunter's as one is an ADN the other BSN. By nature that means each program will have differences related to the type of degree being persued.
The only sciences required for CSI is Bact, A&P I and II, no chemistry organic or otherwise that one can see from the current course requirements, nor math for that matter. Though one must pass the CUNY math placement exam or take remedial classes as part of entering any City U college.
OTHO Hunter being a four year degree there are various math and chemistry requirements (organic and by extension general chem if one does not have the required high school chemistry classes).
Both programs are competitive for entry but Hunter is more so as it is the only BSN undergrad program in CUNY besides Lehman. With only 100 slots for their undergrad program each semester Hunter receives on average >200 (probably much higher) applications, thus getting in is going to really be tough. When the OP says she/he was admitted to Hunter one assumes this to mean as a undergraduate student to the college and not the nursing program itself.
CSI recently stepped up their game in terms of admission GPA so it's pretty much even with Hunter (3.0).
What really matters in terms of choosing between the two programs is what sort of career as a nurse one wishes. If the intent is to go on for a masters and or become an AP nurse, then going to a BSN program and getting the foundation in math and sciences required for any BSN much less MSN out of the way can make sense. Also Hunter's nursing program will offer the required nursing research, theory and other classes that are building blocks to going on for a graduate degree.
The other thing to consider is right now BSN grads do seem to have an advantage in terms of hiring over ADN. NS-LIJ who owns two SI hospitals issued a statement over a year ago that they would be requiring all new nurses hired after a certain date (2012?) to either have a BSN or obtain it within several years after hire.
While a 3.5 GPA is rather excellent for CSI, it is pretty average these days for Hunter's nursing programs. It does seem that at the latter a majority of applicants are at or near 4.0, and yet still some don't make the cut for entry.