Where to honour deceased child in Tokyo?

I will be visiting Tokyo for business in the second week of November. My oldest son passed away a little over three years ago and I try to honour him when visiting a new country, by leaving a token, lighting a candle or some other form of remembrance.

I only have Saturday morning free in Tokyo.

Is there a recommended place (temple?) where I might honour my son, and are there any recommendations on how to do so with respect for the Japanese culture?

You can honour any place for your deceased child.But mosque, Church, pagoda,temple considered as best.According to my holy Book:Our creator is full of shy.He feels shame,if any of his creation demand anything from him.But he ignores to reply.

Just around where in Tokyo will you be?
A temple would be an appropriate place. There are places where you can purchase an incense stick and burn it, just like you might light a candle at a church. Temples are places where people pray for the souls of those that went before them.

Thank you. I'll be staying at Tosei Hotel Cocone Kanda. It was suggested that Zozoji temple would be a good place to visit?

Yes, Zojo-ji (Hamamatsucho, Onarimon or Shiba Koen station) would be a good place too.
Considering that you�fll be staying in Kanda, on the rather eastern part of Tokyo, Zojo-ji and Tsukiji Hongan-ji (Tsukiji) come to mind. Senso-ji (Asakusa) would be a bit too busy and touristy for your purpose.