<<"if we were to do the Thun or Brienz boat ride which one should we do? If I take a boat from Interlaken West to Thun how do I come back from Thun?">>
Note the post from Alpenrose.
None are available on Lake Brienz until after you leave.
That helps narrow the choices.;-)
You are looking at exactly the correct timetables for Lake Lucerne. You know when you will be there and how much time you have.
If you can squeeze in a trip as far as Beckenried, that would be nice. It gets you almost into the southern arm of the lake ( the Urnersee) . The very southernmost part as far as Flüelen is the most scenic, I believe. You don't have time to do that. The shorter trips to Alpnach aren't too bad...you get to see a bit of the nicer mountains and can catch a train back to speed up the process. Kehrsiten-Bürgenstock is really a shuttle boat to/from the base of the funicular that goes up to the mountain resort on top of Bürgenstock. That might interest you. Quick up and down. A couple of pictures in the thread about Hammetschwand linked below are relevant. In the one with the arrow pointing to Hammetschwand, look to the right to see the Bürgenstock hotels in the saddle of the ridge. They have been replaced by newer fancier ones.
After Beckenried, I'd pick Vitznau. 1 hour each way. frequent service.
I posted a description of a hike around Treib, (which is near near Beckenried), and Bauen.
There are pictures in there showing something of the scenery in that area. You won't have time to do the hike. If you want o add time taken away from the city of Luzern, you could take the boat further to Treib, ride the funicular up to Seelisberg, turn right around and come back dow, then take a boat back to Luzern, or across the lake to Brunnen, train back to Luzern. That would take quite a bit more time.
You won't have time to go to Hammetschwand. There is a necessary walk of 30 or so minutes each way.
Check the images.
It would be simpler if you could find a good time on the Thunersee. Fewer choices., closer to your base. Possibility of completing the journey around the lake by train or bus.