In case you aren't aware of it, Mobile Plaza Akihabara is the THE place for mobile imports. From classic Palm to the latest overseas models, they have just about everything. I think I saw an Apple Newton. The best thing is they have accessories: cases, batteries, docks for stuff that was never released in Japan.
I just picked up a Mugen Power 1600 mAh battery for a Nexus S for ¥3,980 (plus tax), which isn't a bad price for a brick and mortar shop.