Use JPQL. A native query is or should be passed to the database exactly as you have created the SQL string, and unless your driver can take a serialized collection and understand that the single parameter needs to be interpreted as many, it just won't work. The collection you pass in needs the SQL expanded from (?) to (?, ?,...) based on the number of elements in a collection, and JDBC drivers just are not able to do this, and JPA providers are required to execute the string as is.
A JPQL query allows the JPA provider to create the SQL it needs dynamically based on the list passed in, so it can expand the collection for you.