What is the height above ground of NCEP/NCAR Reanalysis 1 variables?
The height coordinate varies and is described for the various variables on the site you link.  For example:


  Levels:
  
  Surface or near the surface (.995 sigma level), or entire atmosphere (eatm)


and


  Levels:
  
  17 Pressure levels (mb): 1000,925,850,700,600,500,400,300,250,200,150,100,70,50,30,20,10
  Some variables have less: omega (to 100mb) and Humidities (to 300mb).


For the pressure levels coordinate the height above the ground is variable and dependent on atmospheric conditions.  The sigma levels are terrain following and flatten out with height and will vary with local topography. (see this for more info)

You can estimate height using the hypsometric equation, or use the geopotential field from the data to determine the height at specific grid locations (it will vary horizontally).  For processing, I would recommend using the geopotential data since it is available for each of the vertical coordinate possibilities in this dataset.