Google would be of fantastic help, you just need to use it properly.

I don’t know any guides in Tokyo, but I do know how to hook up with people I share interests with. Google is an amazing resource for that.

First way to find someone to point you to “cool” is to think about what it is that you find “cool”. Tokyo is a maelstrom of niche shops, cafes, bars and restaurants. Many don’t bother with servicing 90% of potential clients, they just figure out what 5% like (or 2%, or 1%) and cater to that group. Tokyo is so vast, a small subset of people can sustain a small business.
As well as individuals, groups meet up in these places and many of those groups enjoy meeting up with like minded visitors. A decade and a half ago, before the whole blogosphere took off and when translation tools barely existed, I used to talk to people and find information at Record Shops. It’s much easier now.

Alternatively, just comb through the NHK “Tokyo Eye” series on YouTube. It covers lots of interesting neighbourhoods and points out some quirky and beguiling places. But stick to the recent episodes as information about Tokyo can become out of date very quickly (I called Tokyo a maelstrom for a reason!)