Lay the swatch flat.  You may gently hand block the swatch by stretching it horizontally, vertically, and diagonally a few times before you measure it, but you don't want to distort it too much.  

I like to start in the center of the swatch and measure how many stitches are in one inch.  Then I measure in one or two other spots.  I'm always surprised by how the tension can change over a few rows!