If you are logged into the server via ssh now, here is the command you will want to enter via the command prompt. First, you will need to start the mysql command line client with this command:
mysql
After you enter this, you will see a prompt similiar to below:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 2
Server version: x.x.xx-community MySQL Community Server (GPL)
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql>
Once you are at a MySQL commad prompt now, you will need to select the database for which you want to repair the table on. For example:
mysql> USE cpanelusername_databasename;
Database changed
You are now actively using "cpanelusername_databasename" replace those variables to match the cpanel username and database name you are wanting to repair.
Now you can issue the repair operation. Here is the command:
mysql> REPAIR TABLE `table1` , `table2`;
If you want to repair more than 2 tables, you would just add them in the order with a comma "," then put the table name(s) in single quotes.