If you don’t mind doing a few laps, a run around Komazawa Olympic Park is an inspiring spot for a run. The park is an oval-shaped, tree-lined recreation sector in Setagaya City, about three trains stops from Shibuya. It features numerous facilities that were used for the 1964 Tokyo Olympics. While there, enjoy some of the other sports facilities!  More info.  There are public restrooms and drinking fountains. 

For running, there are numerous paths around the park, including a dedicated ‘jogging/cycling course’. A loop around the perimeter is ~3 km, but you could add ~1 km or so on the interior paths. There;s also a running track.