Comparing crime rates between countries is a great way for tabloids to get a shocking headline, but it's not usually a very effective method of actually seeing which country has more crime, because, as you say, definitions and recording methods vary widely - it's why the likes of the Daily Mail will tell you that Sweden has the highest levels of rape in Europe, when in fact they have similar incidences to the rest of Europe, but have a higher reporting rate and a radically different (and much more accurate) system of recording.
Even when comparing murder rates, there are things to take into account, such as the criteria used to establish whether a death is treated as murder (as opposed to manslaughter, suicide or accidental).
The only way to accurately gauge which city is safer would be to perform a series of controlled studies and surveys, taking into account not just incidences of crime, but how safe the general population feel in the city.