I haven't read the books yet (although I got Blood of Elves and Time of Contempt), admittedly I haven't exactly been an avid book reader for the last couple of years(aside from work related literature), and fantasy isn't really my preferred genre, but TW got me interested in its world and characters far more than any other fantasy game I played, so I will definitely try to read the books at some point(hopefully in the near future when I acquire the rest of them).
That being said, I choose Triss, her character really resonated nicely with me in TW2 (I even liked her in TW1), and after doing some lore research I started liking her even more, she is a flawed character, and underneath that nice and sometimes naive looking exterior lies a complex character, prone to betrayal and ready to do some morally wrong and shady stuff to achieve her goals. But still idealistic by nature and in general a good person( by Witcher standards). So I was biased toward her before TW3, I knew that if the game gave me choice, no matter how Yen is presented, I will still choose Triss. Probably some of the book readers had similar bias toward Yennnefer. I do not regret that because I really liked Triss in TW3.
Yennefer on the other hand is also a fascinating character, if I was given a choice between her and any other romancable character I've ever seen in a game, Yen would have won by a mile. I like her wit, the way she interacts with Geralt and makes fun of some of his awkward habits, her determination to do everything it takes to find Ciri, I was all for using the mask, necromancy and the destruction of the garden, the way I play Geralt, given the choice I would have done the same. Her excitement when she first saw Ciri is still one of the most memorable moments in the game for me. I would also never deny that by the lore she is Geralt's one true love.
I don't think my preference will change when I read the books, I will definitely do a Yen playthrough sometime into the future (around second expansion), but Triss will most likely remain the right choice for my version of Geralt. If I had read the books before playing the games, or just before playing TW2, it is not unlikely I would prefer Yennefer instead.