The per capita murder rate is quite low for a large city. New York City's population is so much higher than any other city in the country that it tends to skew your perception.

Having grown up in the NYC media market, it's a lot better now than it was in the late 80's/early 90's when there were a few murders per day.

http://en.wikipedia.org/wiki/Crime_in_New_York_City

In 1990 there were 2245 homicides, 4x more than last year. That's scary.

The map shows 3402 homicides from a 6 year period, an average of 500 a year.