I agree with bbunch. Wooden is definitely more competitive and thus, more difficult to build a good program. Naismith is also competitive, but it's a bit easier to win there. So, it just depends on your preference.
As far as conference recommendations...I would also agree with bbunch. New Jersey is one of the top 7 conferences in Wooden, and one of the few that has an opening right now. Can't go wrong with New Jersey. Four other top conferences that have one opening each: Michigan, Midwest, Upstate (3 of the "Big Four") and CCIW (mid-major).
The midwest region is an absolutely brutal place to recruit in Wooden, so if you're not into that sort of thing...I'd recommend New Jersey or Upstate. New Jersey would be my recommendation because Upstate is the "Evil Empire" of Wooden. They've been the best conference for the past 40 seasons or so, and we all are constantly trying to dethrone them. So, don't join the dark side! :)
As for Naismith, CUNY and Northwest have openings and are two of the top 7 conferences currently. They tend to be fairly active and competitive....though not as much as the Wooden conferences I mentioned, imo.