I hadn't read the article you're referring to, but I just found it online through accessmylibrary.com: "The Movie Lover," from the 20 Oct. 2003 New Yorker. Pretty interesting stuff, although I don't think your recollection of what Tarantino said regarding the reception of Jackie Brown is accurate. The closest thing in the article I can find to him discussing the reaction to the movie is this:
One of the many personal genres that Tarantino has made up is "hangout movies"--movies whose plot and camerawork you may admire but whose primary attraction is the characters. A hangout movie is one that you watch over and over again, just to spend time with them...
"Reservoir Dogs" and "Pulp Fiction" aren't hangout movies, but Tarantino hopes that "Jackie Brown" has become one. He hopes that people will see it the first time just to get the plot out of the way, and then, whenever they feel in need of a certain sort of company, watch it again. "Jackie Brown," he thinks, is the sort of movie that people tend to like better the second time, even better the third time, and maybe even better the fourth time. "You don't watch it four times in a row," he says. "It's just that, for people who like it, I really wanted to give them a gift that they could watch for the rest of their lives. Every two or three years, put in 'Jackie Brown' again, and you're drinking white wine with Jackie, and drinking Screwdrivers with Ordell, and taking bong hits with Melanie and Louis."
That doesn't sound to me like he was disappointed with its reception. Maybe you're thinking of something he said in some other article?
As for Jackie Brown being his best movie, I do love it, but I think Pulp Fiction is still clearly his best. In the long video interview with him on the Jackie Brown DVD, he said something like, "Everyone's talking about how there's this serious, adult stuff in one of my movies now for the first time. It's nice to hear, but then you go watch Pulp Fiction again and see it there too." I've probably mangled the quote pretty badly, but he was definitely expressing the belief that he wasn't doing anything particularly more "mature" in Jackie Brown, because he felt that he already showed that side in Pulp Fiction.