So I was able to figure this out by manually configuring HikariCP in a java configuration file. That allowed me to get a reference to the Spring Boot MetricRegistry, which I could then set in HikariConfig. Here's my configuration class: 
@Configuration
public class DatasourceConfiguration {
    @Value("${spring.datasource.username}")
    private String user;
    @Value("${spring.datasource.password}")
    private String password;
    @Value("${spring.datasource.url}")
    private String dataSourceUrl;
    @Value("${spring.datasource.driverClassName}")
    private String driverClassName;
    @Value("${spring.datasource.connectionTestQuery}")
    private String connectionTestQuery;
    @Autowired
    private MetricRegistry metricRegistry;
    @Bean
    public DataSource primaryDataSource() {
        Properties dsProps = new Properties();
        dsProps.setProperty("url", dataSourceUrl);
        dsProps.setProperty("user", user);
        dsProps.setProperty("password", password);
        Properties configProps = new Properties();
        configProps.setProperty("connectionTestQuery", connectionTestQuery);
        configProps.setProperty("driverClassName", driverClassName);
        configProps.setProperty("jdbcUrl", dataSourceUrl);
        HikariConfig hc = new HikariConfig(configProps);
        hc.setDataSourceProperties(dsProps);
        hc.setMetricRegistry(metricRegistry);
        return new HikariDataSource(hc);
    }
}