We decided to take the train to Thun and ride the boat back to Interlaken, based on the late time for the first boat departing out of Interlaken. With our Swiss Travel Passes, the boat and train were both free.
This boat stops hourly in many of the towns, which allows more flexibility than we found in our Lake Brienz boat day (that one is every 2 hours). We found Thun itself a bit too busy for our taste, and ended up spending a lot of time in Oberhofen to visit the castle and then swim in the lake (it was during the late June heatwave). The boat from Oberhofen to Interlaken was just under 2 hours.
Interestingly, I saw many comparisons which say that Lake Brienz is more picturesque than Lake Thun due to being more green in color. Honestly, they were pretty similar - we had bright clear days for each lake trip and the water was an amazing bright blue-green for both. I think the choice would come down to how much time you have (Lake Brienz smaller) and which lake towns catch your interest. Both were awesome.