I noticed the same thing, the NRC ranks UCSD lower than US World news and report (I've never looked at UCSC).
Unfortunately I have no knowledge of either program but that won't stop me from giving out some generic advice! First off, its good to visit campuses, its good to like where you're going to work for 5-7 years.
You should also look up the research programs, see what the active research areas of the professors are and if you're interested in them. This is of primary importance.
Also these rankings aren't always trustworthy. You can find plenty of critiques of them online. If you want to get good information on the programs, ask around in your department. Maybe a school has a better representation within the CME community but you wouldn't know about this from just the overall rankings.
Personally, I prefer the NRC rankings over the US World news and report rankings, but its always good to take them with a grain of salt.