I've only been to Tallinn and Helsinki so will tell you what I know about those 2 places. I spent a full week in Estonia in early Sept 2013--I'm part Estonian so wanted to visit numerous museums, historic sites and took a couple of day trips as well as the ferry to Helsinki for a day. September is still lovely weather there with just a chance of rain. I stayed at a boutique hotel called the Savoy, in Tallinn's beautiful Old Town but just on the edge of the New Town so easy to walk to many things as well as catch a bus or tram, very nice hotel--clean, well-kept, lovely room, great bar and excellent restaurant. Breakfast was included and everything was good. All in all it was one of my most enjoyed vacations, nice mix of things to do and see plus time for relaxing, and I do plan to return in a couple of years.
If you're not big on museums you could certainly get away with a full day (as in 2 nights) in Tallinn, lots to explore in the charming Old Town on your own or take a tour--I highly recommend EstAdventures for walking tours as well as day trips, I went to Lahemaa National Park on one and on another to the western area, including Haapsalu. Beautiful countryside, lots of ruins and manor houses to tour. I also rode the bus to the outskirts for the Rocca al Mare Outdoor History Museum--lots of walking to see numerous original Estonian houses from various periods in history, then to their zoo--enjoyable but not a must-see. If you're a fan of hand-made things you'll find several co-ops in Tallinn, plus as a knitter I knew I'd need to buy some of their famous lace scarves and mittens--just avoid the outdoor market stalls as that stuff is all machine-knitted.
I took the Tallink Silja ferry to Helsinki for a full day, about 2 hours. I recommend at least a full day in Helsinki as well, quite a charming and cosmopolitan city and I only scratched the surface. Knowing what I know now I'd have moved camp to Helsinki for 2-3 full days and flown home from there. From the ferry terminal I caught a bus to the Esplanade for the outdoor market and to catch a smaller boat to Suomenlinna sea fortress, lots to see there but I spent perhaps 2 hours since I wanted to see more of Helsinki and not miss the return ferry to Tallinn. I didn't visit any museums, instead just walked and admired their architecture and shopped a bit--big fan of Moomins and Marimekko.
Looking at your itinerary, I'd suggest starting or ending in Tallinn as it has a pleasantly low-key feeling for a capital city and the airport is ridiculously easy to get to and from, 5-10 minutes from downtown and the cabbies are honest there. Estonians are as friendly as you need them to be, and lots of English speakers. I don't know if you can still access it, but I did a thorough Trip Report called Glorious Estonia on 9/16/13.