It probably comes down to which lake has more of what you want to see on it.
There are a number of boats on each lake so if you have the day, and it isn't too late in the day, you can get off at any of the stops and get back on the next boat going past, maybe continuing your forward journey or perhaps returning, depending on what you want.
Thunersee has a castle. Brienzersee has a funicular railway which leads to an old hotel and from which easy walks take you behind a waterfall and through beautiful woods and gorgeous lake views.
Thunersee has the town of Spiez and small city (really a suburb of Bern) of Thun which you can explore (up quite a bit from the boat as the boat dock is the lowest part of each).
Thunersee has a bigger area and longer trips, Brienzersee has Brienz at the tip which has wood workers, a steam cog railway - the Rothornbahn - going up a mountain, and is just one train stop from Meiringen which beautiful and has special associations for Sherlock Holmes fans.
Thunersee seems more developed to me, Brienzersee more tranquil.
The canal out of Interlaken into the lake is longer on the Thunersee.
I've done them both, like them both, and I personally prefer Brienzersee because it has more of what I want.
But this is a personal choice to see which has more that you want.
How about starting with the first boat and doing them both?