The best way to get there is by being dropped off after seeing the Salar de Uyuni and nearby Lagunas. It's such a worthwhile trip (see my Uyuni, Bolivia page for the info).
If coming from Chile, the easiest way to get to San Pedro de Atacama is via Calama, a large town/city in Northern Chile. From Calama you can get buses to Arica in the north or as far as Santiago and beyond in the south. Some Argentina bound buses leave from both Calama and San Pedro de Atacama.