Infectious diseases such as Influenza and Ebola pose a serious threat to everyone but certain demographics and cohorts face a higher risk of infection than others. This research provides a computational framework for studying health disparities among cohorts based on individual level features, such as age, gender, income, etc. We apply this framework to find health disparities among subpopulations in an influenza epidemic and evaluate vaccination prioritization strategies to achieve specific objectives. We explore the heterogeneities in individuals' demographic and socioeconomic attributes as the potential cause of health disparities. An agent-based model is used to simulate an influenza epidemic over a synthetic social contact network of the Montgomery County in Southwest Virginia to identify infected cases which are then labeled with a specific clinical outcome by using a predefined probability distribution based on age and risk level. We divide the population into age and income based cohorts and measure the direct and indirect economic impact of vaccination for each cohort. Simulation-based results find strong health disparities across age and income groups. Various vaccine distribution strategies are considered and outcomes are measured through metrics such as death count, total number of infections, net return per capita, net return per dollar spent and net return per vaccinated person. The results, framework, and methodology developed here can assist public health policy makers in efficiently allocating limited pharmaceutical resources.