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They're all pretty well linked under the Niseko United liftpass.
If you're looking at the areas individually, Hirafu/Hanazono is the most extensive, but also the most crowded. Also contains two parks. It has the best nightskiing (arguably in the world) and Hirafu is the biggest and most developed base area.
Niseko Village is smaller, and in the middle, so doesn't have any runs off the peak. It does have the newly opened Mizu no Sawa area which is a great powder stash. You have to sit through a short safetly talk before you ride it, but its worth it.
Annupuri is probably the least developed, and quietest. But has some wicked runs off the peak. The terrain between Moiwa and Annupuri is decent too although I understand it can be a little avalanche prone.
Those are the areas that are covered with a Niseko United pass. But it might be more cost effective to just buy an area pass for the area you want to ride on a particular day. (There's not any huge discount in price for buying a multi day pass over individual day passes) You should also try and get to Moiwa, and Chisennupuri which area smaller, seperate areas but worth a short trip to. Also, get to Rusutsu if you have the opportunity.
Mitch is the man to talk to about Niseko for sure. If you want to know anything about the other resorts in Hokkaido, give me a shout. I've been living here a little over two years now.
Enjoy your trip!