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I do this all the time, making use of migration configuration entities (provided by the migrate_plus module). Define a migration plugin in your migration module's config/install directory, using the CSV source plugin from the migrate_source_csv module - omitting the 'path' source configuration, which will be filled in from the form. Let's say the ID of this migration is example_csv. Create a form with a file upload element (named 'csv_file' in this case), and in the submitForm() method:

  public function submitForm(array &$form, FormStateInterface $form_state) {
    $all_files = $this->getRequest()->files->get('files', []);
    if (!empty($all_files['csv_file'])) {
      $validators = ['file_validate_extensions' => ['csv']];
      if ($file = file_save_upload('csv_file', $validators, 'public://', 0)) {
        $csv_migration = Migration::load('example_csv');
        $source = $csv_migration->get('source');
        $source['path'] = $file->getFileUri();
        $csv_migration->set('source', $source);
        $csv_migration->save();
        drupal_set_message($this->t('File uploaded as @uri.', ['@uri' => $file->getFileUri()]));
      }
      else {
        drupal_set_message($this->t('File upload failed.'));
      }
    }
  }