https://trailrouter.com/ is a website/app, where you can set a “starting point” on the map, and a distance (for example 10km), and it will compute a route for you, as green as possible, not along big roads and so on. Recommended!
浮間舟渡/Ukimafunado
荒川/Aragawa is nearby, one can run along the river very nicely: few cars, no stopping because of traffic lights. No light in the evening/night.
The way is asphalt, but often one can use the grass along the way.
Afterwards a visit in a nearby onsen is great.
overall rating: 5/5
下北沢/Shimokitazawa
Shimokitazawa has just smaller parks in direct vicinity, just good for 30min of jogging.
option 1:
one can run until Suginami Kuritsu Seibiyogo School/杉並区立済美養護学校, use a phone and google maps/yahoo transit as guidance. This first part is just to get to the actual jogging place, takes 25min when running (50min when walking) and is along big roads → not very nice.
actual jogging: along the Zenpukuji River, heading west. Some traffic lights, and the way is stone/asphalt mostly, not very nice.
overall rating: 2/5 (all plain roads would be worse)