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I am currently a 3L and will be working for a government agency for at least 3 years. I would like to have clerking as an option for after those three years. I am trying to determine whether I should take fed courts my final semester or an easier class. Do judges care whether mid-career clerks have taken fed courts or not? Or should I take the course that will give me a better chance to increase my gpa?

Take it because you should know it if you want to be a clerk.

I'd take whatever you think will get you the highest GPA. That's actually probably true regardless of whether you're applying as a student or experienced attorney, but especially I doubt judges will really care what classes you took as a law student when you're applying as an experienced attorney. I mean step 1 when reviewing applicants is often to perform a hard GPA/class ranking cut off.

But I'd leave it to those who have clerked for those judges to give advice.

When my coclerks and I look at apps, we specifically look for fed courts. If it's missing, it can be a real knock against an otherwise qualified applicant—particularly if it looks like the applicant shied away from tough classes to inflate grades. The threshold jurisdictional issues taught in fed courts are so important because courts have an obligation to examine jurisdiction even if the parties completely whiff on it. And few things make a judge happier than when a clerk catches a jurisdictional defect that the parties missed.