You can usually buy manga from any otaku biz site, but I dont like to take my chances over the internet. I have found that large retailers have a somewhat decent selection and usually free shipping.
http://www.rightstuf.com/
http://www.amazon.com
http://www.barnesandnoble.com/
http://www.animenation.com
If you buy from rightstuf, it might be good to join their member program.. you get some really good deals that way.