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Staying around Akihabara could be interesting. The neighbourhoods around it are fun. I like Kanda.
One of my favourite places in Tokyo is the yakitori place just across from Shinjuku station. Go out the S. exit, turn right, and it's at the first corner. I also like wandering around in Nezu and Hongo (Not far from Akihabara) and just popping into little places. Mind you, i'm completely at home in Japanese. Tokyo has some very good Western food, but the good stuff is quite expensive.
Kyoto? I'd say skip it and go to Kamakura, which is one hour from Tokyo station. Like Kyoto, Kamakura was once the capital, and it's temples are also quite nice. It also has nice views of Sagami Bay and Enoshima. (The Hiroshige print "Wave" is a view from a beach near Kamakura.)
There's nothing wrong with Kyoto, but it's not a day trip, and you have only a week. I love the Tetsugakunomichi and Kokedera.
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