Aside from the prestige issue, which is what you're asking for, you may also want to consider the differences in the type of work you'll be doing. The type of writing and research you do will be quite different. You'll also have different opportunities in the type of courtroom "work" you see - hearings and trials vs. oral arguments. In my experience, it seems that many people enjoy one much more than the other.
One other thing to think about - do you know where you eventually want to practice? If you're sticking more locally, then either judge will provide good contacts and will be very helpful later on if they like you and are willing to give you a good recommendation. If you're thinking of leaving the area, however, the federal judge may be more likely to know people outside of NY, at least professionally. (none of this is set in stone of course, as judges at the federal and state appellate level all seem to be pretty well connected).