Japanese are big on food or drink from different places. Whenever someone goes out of town, they usually bring back local comestibles for their friends, family and co-workers: if you go to a tourist spot in Japan or to a gift shop in a Japanese-infested area overseas (e.g. Hawaii) you will see tons of pre-packaged individually-wrapped foodstuffs on sale for this very purpose.
So yes, coffee and chocolates are good, especially if there's a local connection (so if you're coming from California, bring some Ghirardelli or See's). You can also make do with local knick-knacks, like little Statues of Liberty from New York or something like that, but the key is to make your gift somehow specific to the place you come from.
Microwave popcorn and ranch-flavored Doritos seem to go over well too (neither are common in Japan, despite many other American things being easy to find here).