Berne – Thun – Interlaken West – Interlaken Ost – Brienz – Brünig - (Alpnachstad) - Lucerne – Berne [Pepe 2012]

You start in the morning with a train from Berne to Thun. These trains leave at 8:07 AM, 9:07 AM and 10:07 AM etc. I will give you the sample starting with the 8:07 AM train because I think you should start "early":

08:07 AM             Depart Berne on track 5 to Thun
08:24 AM             Arrive in Thun
-------------          (Walk over to landing)
08:40 AM             Depart from Thun on Lake Cruiser
10:49 AM             Arrive in Interlaken
-------------          (Walk over the train station)
10:53 AM             *Depart from Interlaken West to Interlaken Ost on track 1
10:57 AM             Arrive in Interlaken Ost
-------------          (Walk over to landing)
11:07 AM             Depart from Interlaken BrS on Lake Cruiser to Brienz BrS
12:20 PM             Arrive in Brienz BrS
-------------          (Walk over to the train station)
12:25 PM              **Depart from Brienz to Lucerne over Brünig
14:04 PM              Arrive in Lucerne

*You could interrupt the journey in Interlaken and walk from Interlaken West to Interlaken Ost which takes 20 minutes and see a little bit of Interlaken, visit souvenir stores and admire the panorama along Höheweg. You would then continue your journey at 12:07 PM instead of at 11:07 AM.
**And you can interrupt again in Brienz from where you have trains to Lucerne over the Brünig Pass at 12:25, 13:25, 14:25, 15:25 PM etc. The train takes 1 hour 41 minutes to Lucerne (and 1 hour 34 minutes to Alpnachstad).

Now if you want to make this a “three lake cruise” you can get off in Alpnachstad and take the boat to Lucerne which takes about 1 hour. The train and boats are coordinated which means that upon arrival in Alpnachstad you won’t have to wait more than 30 minutes to get a connection to Lucerne. Boats from Alpnachstad to Lucerne leave at 1:40, 3:06 and 4:35 PM. The boat at 4:35 PM is most likely a historic paddle boat steamer. To catch this boat you would have to leave Brienz with the train at 2:25 PM.

And then from Lucerne you have a direct train to Berne at every full hour (6, 7, 8, 9 PM) leaving from track 8. This train takes exactly one hour to arrive in Berne.