You can create a "cc_config.xml" (see http://boinc.berkeley.edu/wiki/Client_configuration or see this thread) with something like

<cc_config>
   <options>
       <ignore_nvidia_dev>NNNNNNN</ignore_nvidia_dev>
   </options>
</cc_config>

You will need to set NNNNNNN to the device number to be left unused. The line containing ignore_nvidia_dev may be repeated if you want to ignore more devices.