The ships do not leave without you. That is something hinted at by the ships to make sure you buy their inflated programs. In reality, the pros who coordinate the schedules from the 4 tour companies know more of when the ship will be cleared to depart than anyone but the harbor master. Lets put it this way, in the last 4 years there has been only one couple who missed their ship and they were exploring on their own with Russian visas and forgot the time. A tour company took care of them by having them waiting at the dock of the next port the ship visited, Talinin.
Any of the independent tour companies can give a wonderful tour which is smaller and more personal, with more sights, activities and less crowds than the ship offerings. The ship sold tours are not bad, just not as good. That is understandable when 2000+ plus people have to go on the same schedule and routes in 40-80 buses, you can imagine the design of the program needs to accomodate the complexities of logistics of that many people, and less on the actual touring experience. I think the big bus tours do a surprisingly good job of giving an overview of this unique city. But I also know what a smaller group with more personal attention can do to make the whole experience unforgetable.
When I have relatives or friends visit here, I would need 7 days to show as much to them as they would get from a 2 day intensive custom tour from the pros. Even when visiting by myself to museums the maximum number I can get in per day is two, regardless of how carefully I plan. And I know how to get around this city very well and can read the signs in Russian.
Whatever you choose, I will wager that you will come back here to report that visiting St Petersburg was the highlight of your Baltic cruise and quite possibly any cruise you've done.
Have a great visit