I think you would want to do something like this:
<?php if( have_rows('workshops') ): ?>
<?php while ( have_rows('workshops') ) : the_row();
// assigns checkbox value to var
$location = get_sub_field('checkbox'); ?>
<div id="boston">
<?php if ( $location == 'boston' || $location == 'both' ): ?>
// boston information
<?php get_sub_field('title'); ?>
<?php get_sub_field('link') ?>
<?php endif ?>
</div>
<div id="newton">
<?php if ( $location == 'newton' || $location == 'both' ): ?>
// newton information
<?php get_sub_field('title'); ?>
<?php get_sub_field('link') ?>
<?php endif ?>
</div>
<?php endwhile; ?>
<?php endif; ?>
Also you probably want your radio button choices to be flipped:
boston : Boston
newton : Newton
both : Both
