Most routes to Atins pass through Barreirinhas. From there, regular 4x4 trucks run across the sand roads to Atins, and boats travel along the Preguiças River. The 4x4 trip is faster and more direct; the boat is slower but turns the transfer into part of the journey.
From São Luís, start early if using public transport. Vans and buses can get you to Barreirinhas, where you still need to connect onward by 4x4 or boat.
Do not arrive at the beach landing without arranging onward pickup. The "port" is basically a drop-off point on the sand, and walking from there with bags is a poor idea.