Odaiba and RAinbow bridge
For a 12-15k run, and to get a breathtaking view of Tokyo bay from the Rainbow bridge: make a loop from Tsukiji market to Kachidoki, to Harumi to Toyosu and then go to Odaiba. If you want to run more, you can circle odaiba and then cross the Rainbow bridge, run in front of Hamarikyu park and then get back to the market.
the nice thing is that you do not have many red lights not too much traffic. You can breath oxygen and not carbon dyoxide.