Using the JPA EntityManager and the JPA Query object, how can I override something that has the annotation @OneToMany(fetch = FetchType.EAGER) to be fetched lazily in a quer
Look into Hibernate Fetch profiles, or JPA Entity Graphs. This problem has been solved since you've asked the question in 2012.
There is no way to do that, even with the native Hibernate API. If an association is defined as EAGER, it will always be eagerly loaded, and there's no way to change that using a query.
The reverse is not true: you can eagerly-load a lazy association using a query.