There's some meta-turning (if that's the proper turn) feats in Defenders of the Faith that allow for controlling either more or higher-level undead. I don't have the book with me right now, though.
If you're thinking of the Animate Dead spell, I know that it does have a control limit. Perhaps you could come up with some more powerful versions. Othewise, my advice would be to do it hierarchically, like they used to do in basic D&D. You're uber- necromancer controls the the more powerful undead lieutenents (say, for the sake of argument, vampires); the vampires in turn several lesser undead (say, ghouls and mummies), who in turn command the actual hordes like sergeants. There's no hard and fast rules for this that I'm aware of, but it shouldn't be too hard to work something out. This has the added bonus of allowing the villains to "level" with the characters- they could track down the source of the local undead problems only to find out that the vampire is working for someone else.
If all else fails, you can just come up with some sort of plot item, like a minor artifact only usable by insane necromancers who have performed great rituals, or something. Clunky, but works.