They shouldn't. Their numbers should be based on FBI Uniform Crime Reports stats that are submitted by the cities themselves. I'd be interested in taking a look at the sources you've mentioned, though. Only 10 cities in this country have more than 1m people. Out of those 10, Las Vegas and San Diego are the only ones that have lower homicide rates than NYC.
A few points: 1) A frisk is NOT a search, its a pat down. 2) What major city has a lower murder rate than NYC? 3) The proportion of those frisked and those convicted of crimes are the same when based on race and ethnicity. 4) The REAL Constitutional question arose when it was disclosed that the NYPD had complied computer data based on those frisked. Therefore, the NYPD has a file on you even if you never even been accused of a crime.
http://en.wikipedia.org/wiki/United_States_cities_by_crime_rate
It uses FBI data.
If you throw in cities which are close to 1 million there are several more added. San Antonio is only slightly higher and it has the significant impact of being close to the border.
But seriously, you folks must really approve of the job Bloomberg is doing.