The best way to get there is to arrange a taxi ride (book it trough your hotel for a block of hours). There are two reasons for this:
1) Getting to to the site requires driving on an unpaved road which is better to be left to the locals, unless you know what you’re doing.
2) The surrounding areas are considered ‘Area de conflicto’, disputed areas. Basically the two neighboring municipalities are disputing over who should administer entrance to the site. So you might find yourself stopping at an improvised checkpoint (or two), managed by the locals, asking for a transit fee (or two!) . All this is easier when managed by a local driver.
The locale is stunning, surrounded by beautiful valleys full of cacti, maguey plants (a form of agave used to produce Mezcal) and dwarf palm trees.
There are two possible roads leading to Hierve El Agua, ask the driver to go up the mountain using one and come down using the alternate one, both slopes are beautiful and completely different.