I'd say having the club included would be a nice addition to your stay. Mark Hopkins is more of a classic feel on top of Nob Hill. IC SF is more modern and near the convention center. With that said, if there are any conventions in town (much less Oracle which eats up rooms in the entire Bay Area!) it can get quite crowded.

I have stayed and know the staff at both and can say that you will (hopefully!) be happy no matter which one you choose. IC SF is near the Westfield shopping center and public transit. IC MH is on the top of the Hill near a Cable Car route (and a bus 1-2 blocks away).

I'd look into Ambassador status to get the room upgrade, or at least a higher floor room at either property. Well worth it for that length of stay.