You can, but it is not recommended to repair hard-drives while connected via USB. If you want to check the drive's physical integrity, use HD Tune's full error scan instead. It will report errors if any, but it will not alter your data like chkdisk. If you want to actually repair the data integrity, it is better to connect the driver directly to an available SATA port of a working system and then run repair tools. This will prevent accidents that can happen way too easy via USB connectivity.
HDTune link: http://www.hdtune.com