We just returned from the Galaxy Baltic cruise. The only excursion we did was in Gdynia where we took their bus to the city of Gdansk to explore on our own. All the scandinavian cities are easy to explore on your own. Suggest reading Rick Steves' guides. Everyone speaks english and is very friendly. We bought 24 hour transit passes and really enjoyed doing it ourselves. In Waramunde we took the train to Rostock then came back and explored this lovely seaside village.
St. Petersburg, however, is another story. We chose to use a private guide and obtain our own visas. Best decision we made. I can highly recommend Kolya Blotski - firstname.lastname@example.org
Many pax had bought their tours through the internet site in advance but I never saw any tours waitlisted until the day bookings were set to close. I agree that you need to read the booklet carefully and be sure the tour is what you expect it to be.