Good service in Tokyo is considered the standard, already reflected in the price — not something to be rewarded separately. Offering a tip can be seen as implying the price alone wasn't enough, which runs against the local sense of professional pride. Restaurant staff, taxi drivers and hotel staff will often politely refuse a tip or chase you down to return it as “forgotten” change.
There's no percentage to calculate — the guidance is simply not to tip at restaurants, in taxis, or at most hotels. Saying “arigato gozaimasu” (thank you very much) is the appropriate way to acknowledge good service instead.
The main exception is a high-end ryokan (traditional inn), where a small gift of cash in a plain envelope, given at the start of the stay for special requests, is an old custom called kokoroduke. This is different from a tip for standard service and isn't something most travellers need to think about. Tour guides working with international visitors sometimes accept a small tip, but it is never expected — if in doubt, don't.
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