Funny thing I noticed: Spiritomb's moveset actually gets worse after defeating the Elite 4 and then facing Cynthia after the National Dex is gained, as Ominous Wind replaces Shadow Ball.
Spiritomb knows Shadow Ball, Silver Wind, Dark Pulse, and Psychic.
Your Empoleon can actually do a great job in taking down Spiritomb by using a powerful STAB Surf. Empoleon resists all of Spiritomb's attacks, which is why it is such a good Pokemon for the job.
Also able to resist all of its attacks are Probopass, Bastiodon, and Magnezone. Considering their type starts to stack up with what you already have, I would suggest none of these and just rely on Empoleon to win the fight. However, if you want to use these Pokemon then I would suggest using the move Toxic and then start hitting Spiritomb with your STAB attacks, maybe throwing in Protects to Toxic-stall. Make Cynthia use her Full Restores, then repeat the process. Make sure to keep your Pokemon healthy with items. Even a Pokemon around 10 or so levels lower can take down Spiritomb with this.