The small but very fancy rout is around Patriarch Pound. They have some special community event call "Patriki running" (Patriki begut) every Sunday or so. Another place is park behind World Trade Center.
Izmailovskyj park is likely one of the best places, until it gets dark at least. It's just huge, so much it's easy to forget to be in a city. It's possible to run on road and off road. Just kilometers of woods and lakes.