Tallinn is a place to walk around, not do a bus tour. See http://www.brentjes.com/tallinnwalk.html for a good walking tour. Copenhagen - I saw the bus picking up by the ship, though we also did this city on foot, with a taxi back from the furthest point, Tivoli Gardens.
There is a HOHO bus for Tallinn but by the time you've walked the long pier from ship to buses you are almost at the old town! also it cannot take you around the most interesting part .
Tallinn is very easy to walk around and a bus wouldn't be able to get into all the narrow streets anyway. You don't need an excursion for this port.
Last year in Copenhagen, we did the Red Bus tour am. and then pm. caught the tourist boat by the little Mermaid. Takes you around parts you never see from the road. Got off in the centre and later caught the boat back. An excellent round trip.
Didn't see an open top bus in Talin, but easy to walk. Copenhagen. Did the open top bus (stop near the port) in the morning, then walked to all the places in the afternoon after havin lunch on the ship.