http://www.ebookjapan.jp/ebj/comic_magazine/ is currently my go-to place to buy ebooks for manga magazines, tankobon, and light novels.
Pros:
- They accept my non-Japan credit cards.
- They release ebook manga magazines online (ie: Weekly Shonen Magazine) at the same time as they release in Japan. There is no need to wait for the release even though I don't live in Japan.
- Their selection is ridiculously large. They literally have everything you can think of.