A lot of people aren't aware of the 72 hour visa free option if you use the St Peter Line ferry. You really don't have to have a guide like when you arrive by cruise. You do have to book their "city tour" which is just a shuttle to their hotels. This link explains the rules:
I did the 72 hour visa free option on the St Peterline Ferry back in 2014. For convenience, we just booked our hotel through the ferry line. We stayed at the Sokos Vasilievsky which is not very central but it was a perfectly fine business class hotel with very nice breakfast buffet. It was easy because the ferry took care of the hotel paperwork we needed on entry and the shuttle dropped us off there. There are some posts on tripadvisor that explain what you need if you decide to book your own hotel.
We did the following:
Day 1 - Arrived and took shuttle to hotel. It was around noon or so by the time we got to hotel. Took metro to Nevsky Prospect and visited the various churches along the way.
Day 2 - Took an organized tour that we booked through TJ Travel and visited Peterhof Gardens, Catherine Palace, and Peter and Paul Fortress. They picked us up from hotel. Guide was very good.
Day 3 - Spent about 3 hours at the Hermitage, had late lunch, and then headed back to hotel to catch shuttle (around 4) back to ferry