For manga, I've always purchased from Barnes & Noble and Books a Million, mainly because they're near my house and I'm more of an in-store shopper, but they've got solid online presences and a satisfying catalogue. Plus, both have pretty good membership reward programs (B&N in particular is $40/yr and gives you 10% off pretty much everything, free shipping, and a $5 reward for every cumulative $100 spent, plus some other stuff).

And if those places don't have what I'm looking for, there's always Amazon