mpbear, if you are on a ship's excursion, it will involve coaches, and less use of time to see more. If you book private tours through RSSC, it is going to be VERY expensive. If you book through Red October, you will have neither coaches nor the need to get a visa on your own.

If you want to get your own visa, however, here is the link for information on how to do so through the consulate http://www.russianembassy.org/