If you have a datasource already created it will be in the spring container, so:

@Autowired
DataSource dataSource;

Should do it.

You are saying you have those method below your application main method and you are not autowiring the datasource, so you are creating an instance directly and so that not using the properties. You need to use the singleton object created by Spring. In order to do that you have two possibilities:

First option, and the one you should use, is declare a config class to create your beans:

@Configuration
public class DatasourceConfig
{

    @ConfigurationProperties(prefix="spring.datasource")
    @Bean
    public DataSource getDataSource() {

        // i was hoping this was going to pull my current datasource, as 
        // defined in application.properties
        return DataSourceBuilder
                .create()
                .build();
    }

    @Bean
    public DataSourceInitializer dataSourceInitializer() {
        ResourceDatabasePopulator resourceDatabasePopulator = new ResourceDatabasePopulator();
        resourceDatabasePopulator.addScript(new ClassPathResource("/data/init/initData.sql"));

        DataSourceInitializer dataSourceInitializer = new DataSourceInitializer();

        // the call to the above method
        dataSourceInitializer.setDataSource(getDataSource());


        dataSourceInitializer.setDatabasePopulator(resourceDatabasePopulator);

        return dataSourceInitializer;
    }

}

Using @Configuration, even calling the method directly, as Configuration classes are subclassed at startup-time with CGLIB, you are getting the object created by Spring.

Further information about how Java-based configuration works internally

Second option is auto-wire the datasource in the second method:

@Bean
@Autowired
public DataSourceInitializer dataSourceInitializer(DataSource myDatasource) {
    ResourceDatabasePopulator resourceDatabasePopulator = new ResourceDatabasePopulator();
    resourceDatabasePopulator.addScript(new ClassPathResource("/data/init/initData.sql"));

    DataSourceInitializer dataSourceInitializer = new DataSourceInitializer();

    dataSourceInitializer.setDataSource(myDatasource);
    dataSourceInitializer.setDatabasePopulator(resourceDatabasePopulator);

    return dataSourceInitializer;
}