Have you seen this site? Just search Tokyo. http://www.happycow.net
If strictly vegetarian, I wouldn't advise you to go to any restaurant. I'm lacto-ovo vege, but I decided to be flexible, as long as there is no piece of meat or fish in my dish.
Still, I came across a few dishes that actually had tiny pieces of bacon or ham in them, while you would expect those dishes to be vegetarian and they told me that there is no meat in them.
It was 2005, though. Oh, I went to this place in Sunshire Alpa in Ikebukuro. There was nothing for me on their menu. I only had 40 minutes until going back to work. There was a tomato, lettuce cheese and ham sandwich, so I thought I could ask for one without ham. So I asked to a waitress.
A minute later, she came back and asked if I'm really ok without ham. I said ok, as I was vegetarian and didn't eat meat, or ham. She went away.
A minute later, a waiter came and asked if it was really ok without ham. I said I didn't eat meat or ham and was quite happy with a cheese, tomato and lettuce sandwich. My non-vege boss had been already served with her dish and she couldn't believe what was happening to me.
Now the restaurant manager came out and asked if it was really ok. I said yes, as I already told twice to your staff. He said he would still have to charge the full price and would not been able to give me a discount for not taking ham (!!!). I'd have paid extra if they had let me eat what I asked and go back to work in time.
It might be safe to go for vege options at a macrobiotic restaurant?? I tried one, but I thought my dish was a bit bland. Not sure if many are like that. I haven't been in Japan since.