When I place the code before the closing tag, as recommended, I got some vertical space added interfering with the layout of my page. Looking with firebug into the output, I found that piwik is putting out an img tag.
I suggest adding setting to margin and padding to 0, in line 110 of piwik.js:
So, line 110 (original):
document.writeln('<img src="'+_pk_src+'" alt="" style="border:0" />');
is replaced with:
document.writeln('<img src="'+_pk_src+'" alt="" style="border:0; margin:0; padding:0;" />');