Yes, both the Swiss Pass and the Swiss Saver Pass include free boat trips on Lake Thun, Lake Brienz and Lake Lucerne. Special cruises with dinner or other extras are not free, as you have already seen, but they're discounted in most cases.
The map we link to on the Swiss Pass page is leading. You will get a copy of that when you order your Swiss Pass, so you can take it along while traveling. Most transportation companies see the Swiss Pass as a GA (General Abo) and list their prices as such. The BLS mentiones it like that on their boat fare page as well.
Enjoy the (free!) trips!
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