In the United States, federal policies exist to ensure environmental justice and to protect Indigenous rights. However, the effectiveness of these policies can be influenced by analytical tools chosen by decision-makers to study disproportionate impacts of federal actions, including environmental permitting, on Indigenous peoples in particular and marginalized communities in general. Strong analytics can help identify, early on, communities likely to be impacted by federal permitting and decision-making, providing opportunities to consult meaningfully with communities and address potential injustices or inequities prior to key planning and permitting decisions. In contrast, weak analytics can create blind spots to potential inequities and injustices that may not be revealed until late in planning and permitting processes if at all. Here we evaluate environmental justice analytics used in federal decision-making with particular attention to recent fossil fuel pipeline permitting. Using the Atlantic Coast Pipeline - a proposed shale gas project in West Virginia, Virginia, and North Carolina - as a case study, we identify methodological weaknesses that contribute to decision-making blind spots surrounding environmental justice, focusing especially on implications for American Indian tribes. We discuss findings in the broader contexts of public policies surrounding environmental justice and Indigenous rights. We offer recommendations for policy-makers, regulators, pipeline developers, and members of affected communities.