How to set available options for Comment Per Page select?
Comments per page options are taken from _comment_per_page function and as you can see, are hardcoded:

function _comment_per_page() {
  return drupal_map_assoc(array(10, 30, 50, 70, 90, 150, 200, 250, 300));
}


To substitute this with your own function, you need to implement hook_form_alter, and override changes made by comment_form_node_type_form_alter. Specifically, you need to change $form['comment']['comment_default_per_page']['#options'] and make sure $form['comment']['comment_default_per_page']['#default_value'] makes sense after that change.

To make sure your hook fires after the one by comment module, see Can I change the order in which hook implementation by different modules are called?