Vaccine allocation decisions during the ongoing COVID-19 pandemic have proven to be challenging due to competing ethical, practical, and political considerations. Complicating decision making, policy makers need to consider vaccine allocation strategies that balance needs both within and between populations. Due to limited vaccine stockpiles, vaccine doses should be allocated in locations where their impact will be maximized. Using a susceptible-exposed-infectious-recovered (SEIR) model we examine optimal SARS-CoV-2 vaccine allocation decisions across two populations considering the impact of population size, underlying immunity, continuous vaccine roll-out, and heterogeneous population risk structure. We find that in the context of an emerging pathogen, where many epidemiologic characteristics might not be known, equal vaccine allocation between populations performs optimally in most scenarios. In the specific case considering heterogeneous population risk structure, first targeting individuals at higher risk of transmission or death due to infection leads to equitable resource allocation across populations.