Repair Disk - Start up disk options
One option would be to clone your startup drive to an external disk using something like SuperDuper! or Carbon Copy Cloner. Then you can use System Preferences->Startup Disk to select that external drive as the boot drive. 

Once you've rebooted and are running the system off the external drive you can use Disk Utility to run the repair. After you're done, re-select the internal drive as the Startup Disk and reboot.