Both Basel and Bern are nice cities and have plenty to offer. Basel is more of a "big city" (at least for Switzerland!) and has great museums, but personally I find Bern more charming and attractive. I like the architecture in Bern, the river, the bear park, lunch on the terrace at Altes Tramdepot enjoying the views of the old town, etc. There are a few interesting museums too (Einstein museum, the Alpine Museum, Paul Klee museum), but it is also just a nice place to wander around. The old town is compact and picturesque, just about right for a one night stay. Plus if you overnight in Bern, it's only 20 mins to Thun the next day for your boat ride.
As for Thun, it is a pleasant enough place but probably not worth an overnight in this case. Doesn't look like much from the train station, but if you walk the 5 minutes into town, there is a very lively and pretty center with picturesque wooden bridges (where you can often watch the river surfers practicing), the castle, a small old town, and lots of cafes/restaurants with outdoor seating in the summer months. There aren't really a lot of "tourist attractions" but it's a nice town. You can also walk to the Schadau park, which has great views of the lake and mountains as well as a beautiful historic hotel with restaurant and outdoor terrace. Thun is also a good starting off point for visits to some popular hiking spots, such as the Niederhorn or Sigriswil. Since you are continuing on to the Oberland, this won't really be of interest to you though. In short, for those who have already hit the highlights and/or want to explore a little bit off the main tourist trail, Thun would make a nice half-day trip in combination with something else (or for lunch and a stroll before/after the lake cruise) but for this trip, I wouldn't stay overnight there.