I'm pretty sure this should do the trick:
Sync your 3GS to iTunes one last time. Then, unplug it from your computer and go into Settings > General > Reset > Erase All Content and Settings. After the erase process is finished, you should be at the setup screen (if you're running iOS 5, and I assume you are). Go through the setup process without selecting the option to restore from a backup, and you should find a completely wiped phone. Also, keep the SIM card in until you get past the setup; you'll need it to get past the activation screen. After that's done, take it out and put it somewhere safe, because you may need it again (if you ever need to restore, or even update the device).
When you set up the 4S, just plug it into iTunes and use the backup of the final sync you did with the 3GS. You should get a new SIM card included with the 4S, but if not, just use the old SIM from the 3GS after restoring that one.