The vast majority of travelers here visit Bonampak [1] and Yaxchilán [2] on round-trip shuttles from Palenque [3]; if you’ve only got a day to spend here, it’s the easiest and cheapest way to go, as you don’t spend time or money organizing the transfers, particularly the boat to Yaxchilán.
With more time, you might consider staying the night, and taking the next day to visit places like Lacanjá Chansayab [4] or Nueva Palestina [5]. Two nights or more are recommended for visiting Nahá [6] or Metzabok [7], to leave plenty of time for the long drive in and out, plus at least one full day for the various excursions and other activities available there.
It’s possible to explore the Río Usumacinta Valley [8] by public transportation, though service anywhere off the main highway can be pretty spotty. A rental car or truck, if it’s in your budget, makes visiting the area simpler and much more efficient.
The Carretera Fronteriza [9] now loops all the way around to Comitán [10] and onward to San Cristóbal de las Casas [11], with turnoffs to popular ecotourism destinations like Las Guacamayas [12], Las Nubes [13], and the Lagunas de Montebello [14]—a great option that avoids any backtracking. Frontera Corozal also offers a back-door route to Tikal [15], the stellar Maya ruins outside of Flores, Guatemala [16], if you’re considering heading there.
Links:
[1] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/bonampak-archaeological-zone
[2] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/yaxchilan-archaeological-zone/yaxchilan-ruins
[3] http://www.moon.com/destinations/chiapas/palenque/palenque-town/palenque-archaeological-zone
[4] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/along-the-carretera-fronteriza/lacanja-chansayab
[5] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/along-the-carretera-fronteriza/nueva-palestina
[6] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/along-the-carretera-fronteriza/naha
[7] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/along-the-carretera-fronteriza/metzabok
[8] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley
[9] http://www.moon.com/destinations/chiapas/the-rio-usumacinta-valley/along-the-carretera-fronteriza
[10] http://www.moon.com/destinations/chiapas/the-lakes-region/comitan
[11] http://www.moon.com/destinations/chiapas/san-cristobal-de-las-casas
[12] http://www.moon.com/destinations/chiapas/the-lakes-region/eastern-chiapas/las-guacamayas
[13] http://www.moon.com/destinations/chiapas/the-lakes-region/eastern-chiapas/centro-ecoturistico-las-nubes
[14] http://www.moon.com/destinations/chiapas/the-lakes-region/eastern-chiapas/parque-nacional-lagunas-de-montebello
[15] http://www.moon.com/destinations/guatemala/peten/tikal-national-park/tikal
[16] http://www.moon.com/destinations/guatemala/peten/flores