I would say that of the alternatives, Dune2k (
http://dune2k.com/) is the best.
My experience with Dune communities online has been fairly negative, though, and I think the two pre-eminent communities are.
alt.fan.dune was the pre-eminent Dune community for many years. When the internet and I were young, Dune was one of the best represented fandoms, and the newsgroup seemed thrilling to a thirteen year old. Adults were talking about my favorite book, and taking it as serious literature! Amazing!
It became clear, over the years, though, that afd was an incredibly, incredibly incestous group -- they're a "we exist only to say we're brilliant" sort of a newsgroup. They look down on pretty much anything but the original Dune novels and the Lynch movie vehemently... they hate the Kevin J Anderson books, the recent movie, all the video games, etc all beyond critical reason. Basically, a bunch of jerks pretending to be cultured. (Insult to injury, with an Lit degree and a half behind me I now know that most of what they had to say about Dune in the first place was pseudointellectual crap...)
Dune2k, on the other hand is... young. It's a lot of kids who are still in that pre-reason phase of internet fandom, where the coolest thing in the universe is a battle scene or a video game letting you build a bigger missile launcher. They're a lot more accepting, though, and if they survive for a while they'll be a great place for Dune discussion.
(I'm sure ranting about afd makes me sound like I had some experience there to be bitter about -- I really didn't, I never posted to the group... I just lurked for several years and occasionally go back to see them all stroking their egos over hating the prequel novels.)