The Third Option Is Honto H.O. NTO.

Honto H.O. NTO is a good option if you're not particular about manga or anything like that. Book life offers frequent coupons and sales, which can be kind of addictive. Amazanseo.co.jp has a great selection of English books too. If you don't want to go through the hassle of getting a Japanese VPN and home address from outside Japan, Amazon could be an option.