I loved both of these books. If I had to choose one to be my favorite of the two, it would have to be Sweet Thursday though. I know that sequels are not supposed to be better than their predecessor but I think that these two books are just so good that choosing which one is better lies purely in personal opinion and fuzzy warm feelings.
I feel like I could tell Steinbeck was older when he wrote Sweet Thursday. Both books are wise and have a lot to say about society and human relationships but Sweet Thursday speaks to me more. Maybe just because it is more about love and it has a hilarious masquerade ball scene in it where everyone from town dresses as characters from Snow White and the Seven Dwarfs (but the grocery store owner dresses as Dracula because in his mind all movies are the same).
Also, Cannery Row is a great deal about men and manly things- similar to the arrangement in Tortilla Flat when a group of men live together, work no jobs, but live happily and healthily observing the world at a leisurely pace, but in Sweet Thursday, we take a microscope on the town brothel and discover a strong female character finally in Suzy, a women not meant to be a hooker or hustler.
Life inside the brothels are illustrated again and again in Steinbeck books. Steinbeck seems to prefer to show the human side of prostitutes and see how strong and supportive they are. They are strong women who are part of the community and influence the town (for the better). They also know how to work the system and shut down around the same time every year when people celebrate V-Day, knowing that this outburst of patriotism for some reason resents their kind. Fauna, the second owner of the Bear Flag, is a smart, sympathetic business-owner who everyone seems to respect. Except for the Patron who has taken over Lee Chong's grocery store after the war. The mexican seems to not be as progressive as the other men in town who as a whole seem to respect Fauna and her girls.