Serpi,
The noise marker, using power, average settings, will give you a good noise measurement. The trace does not have to be in average mode, but it may help stabilize the reading a bit more.
You will find most frequencies have a noise figure quite a bit better than our specification. As a spectrum analyzer, we are required to meet the DANL specification at all operating frequencies for the life of the instrument, so padding these numbers a bit is prudent.