Where to populate custom terms in custom taxonomy in plugin?

Hook into registered_taxonomy. This is called after the taxonomy was registered successfully.

Sample code:

add_action( 'registered_taxonomy',  'insert_default_terms', 10, 3 );

function insert_default_terms( $taxonomy, $object_type, $args )
{
    if ( 'your_tax_name' !== $taxonomy )
        return;

    // insert terms
}