They won't be booked, just extremely crowded. People are constantly getting on and off these boats, so it's more like a ferry than a tour. You will be very unlikely to get a seat in 2nd class unless you hit the first boat in the morning and don't get off or get up to look around giving up your seat. You're more likely to get a seat in 1st class on the roof. You don't have to show any ticket/pass when you board the boat. A worker will come around sporadically checking tickets/passes once the boat is moving.
In terms of what is more "spectacular"....it depends on your definition. If all I was doing was riding the boat and not getting off, I'd do Lake Brienz because the water color is more dramatic aqua and it's a shorter ride from one end to the other. If the idea is to hop on and off, I like Lake Thun because of the castles at Spiez, Oberhofen & Thun. Typically if we do Lake Thun we'll train to Thun and ride towards Interlaken West with stops at Oberhofen & Spiez, but if you want more time to explore Thun, then do it the opposite direction and then have dinner on the lovely riverfront in Thun. The homemade ice cream at the Spiez boat dock is excellent and the lakefront promenade around the Oberhofen castle is lovely. We usually go swimming with the swans there every summer.
The highlight stops on Lake Brienz are Iseltwald, which has become a tourist site because of the Korean netflix show (Crash Landing on You), so what was once a very sleepy little hamlet is now full of tour buses and people paying to go out onto the dock from the show to take their photo. The other main stop is Giessbach for the waterfall and historic hotel/funicular. Another option for Lake Brienz is to train to Brienz, do the Brienzer Rothorn roundtrip and then take the boat from Brienz back to Interlaken Ost.