Each issue has 3 covers (issue 1: Mal, Jayne, Inara -- issue 2: Kaylee, Zoe, Book -- issue 3: Wash, River, Simon). They'll probably become quite collectible, so why not get one of each? I've been getting 1 of each cover of each issue to keep in the bag, and 1 extra of each issue to read.
Anyhow... they should be available in all good comic book stores, but I very strongly recommend ordering them from the Poplollies Serenity shop.
Poplollies is an on-line store run by a couple of really cool Browncoats. They're great folks, provide excellent service and ship the comics in bags with back-boards so they're pristine when they arrive. Even if I didn't know the owners and know they're wonderful people, I'd be super-impressed with how quickly they arrived, how pristine they were, etc. :) I believe they also have all covers of all issues in stock, which most comic book stores do not.
[Edit: Apparently Poplollies is temporarily out of stock of the Mal cover of issue 1, but I think you can still order it and they'll send it when they have it in stock]