WOW. I've sure learned a lot in just a couple of weeks! Mainly, that I should have started all of this a long time ago! However, I did find that you only need a Russian Visa if your stay is longer than 72 hours. No one on a cruise will be in port longer than that (unless you miss the ship departure). We will only be in port two days, so any private tour group can arrange for the same short term Visa that you get through the ship.
I have seen very positive reports regarding Red October, DenRus, Alla and Baltic Tours! Prices vary widely, but each of them offer smaller groups, with English speaking guides and at very attractive savings over the ship's tours (featuring high prices, large groups and crowded buses).
Timecop...hope this additional info is helpful in your planning! And thanks to all others for their input. Departure from O'Hare in two weeks!!!