I think the OP should listen to ronjeremy.
While everyone--including the OP--seems to be focusing on the prestige factor, the OP states that he or she wants to enter academia one day.
A federal district court is a trial court. You are going to see a lot of pretrial practice--disco, joinders, class action certification, etc. You will generally assist a judge or a group of judges writing orders and researching the law. You may see some very interesting trials.
The Supreme Court of California is an appellate court, the highest court in California and--whether you agree with its decisions or not--one of the most influential state supreme courts in our country. Just look at any casebook. Many opinions come from that court. I don't think anyone would say that a clerkship there is not prestigious.
Further, at an appellate court you will witness some of the brightest judges and attorneys arguing why law should change or stay the same. You may see issues of first impression. Regardless, you are going to see big-time policy issues being debated.
To me, if the OP wants to enter academia, the Supreme Court of California is the way to go. I think the trial/appellate distinction is of greater relevance than the state/federal distinction.