Both will use a JDBC connection pool to manage your connections so I would not expect there to be a major difference in performance.
Method 1 doesn't use any of the JOnAS features to create or manage the JDBC connections + pool. The same configuration will work outside of the application server. This is useful for testing without the requirement to deploy to the application server.
Method 2 will use the JDBC connection pool configured and managed by JOnAS (the application server).
Typically, if you have made the decision to go with an application container (e.g. JOnAS, JBoss, Websphere, etc) it is usually a good idea to let the container manage the resources that you use. That's what they are designed to do, and you may require some of the advanced features for managing the configured resources. There is also the benefit that your application doesn't have to know what implementation/driver is being used (or username/password, so you can deploy your EAR/WAR to different application servers without having to change your application configuration. These details are configured in the server instance instead.
If using Method 1 inside an application server, the server will have no control over the threads being created, because it knows nothing about them.