I am not entirely sure how US News or NRC come up with their rankings. It is entirely possible that CUNY does well on one set of criteria and poorly on another. You can even see that in the NRC rankings itself. NRC's regression-based ranking of the CUNY Graduate Center is 46-80, significantly above the survey-based ranking of 103-120.
I don't know how strong CUNY is academically, but there are a few other statistics from PhDs.org that worry me. I'll put in parentheses the corresponding numbers from the University of Nebraska at Lincoln, ranked # 68 by US News and 66-99 by NRC.
Percentage of first-year students with full financial support: 27% (96%)
Percentage of graduates still seeking employment at graduation: 41% (6%)
Median time until graduation: 8.1 years (4.8 years)
If you believe the numbers above, CUNY doesn't look like a place that supports its students very well. It also doesn't seem to attract a very talented pool of graduate students. Most math graduate programs, including Nebraska, have an average quantitative GRE score above 790. CUNY's is 751.
All of this may not matter so much if there's a strong research group that's supporting you. But you'd have to talk to someone who knows the program very well to find out if there are subgroups that are academically stronger and more supportive than the program as a whole.