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.
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.
It depends on where you live really. I would say any park near your place is a good place to go. My favourite place is Gorky Park — it has a nice, 7 kilometer long river embankment that is open 24/7. No cars allowed, so it is all yours. A lot of runners go there, which gives you a nice sense of community and other runners often smile and wave at you. The scenery is great there, the air is clean, it has public toilets and vending machines with water every 1-2 kilometres, so I highly recommend it!