This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
EJB is by now up to 3.1, which is just a minor update to EJB 3 - so that book should be fine.
If you like the Manning "... in Action" books, then "Java Persistence with Hibernate" is available, although that covers an older version of Hibernate that implements JPA 1, not the current JPA 2.
And speaking of JPA, you may want to consider learning JPA instead of Hibernate. It's generally better to go with standard APIs than to use specific implementations; most people don't need what the Hibernate API offers over JPA 2, and you'd lose the ability to switch JPA implementations.