Can't help with the wineries part of your question except to say google wineries in Crete and you will come up with all sorts of information as to which are open, when and location. Most seem to have Heraklion as their base...
Vathypetro is about 15kms south of Knossos. Leaving Knossos you keep on the road through the village until you come to Archanes there are actually two villages, lower (kato) Archanes and Archanes). I was with a group and we stopped for lunch here - I can't tell you the name of the restaurant but it was upstairs and overlooked a small square in Upper Archanes. Vathypetro is 5km further on. As I recall the site was not well sign-posted; you have to park by the roadside and walk along a track. Its a stunning setting, high on a hill overlooking the valleys and mountains, including Mt. Iouktas, birthplace of Zeus.) The site is quite small, some room blocks and a room containing the remains of an olive press but the setting is worth the trip.
I was there in late April and the wildflowers were out but we also landed in the middle of a thunderstorm and torrential downpour so lunch at Archanes lasted longer than originally intended!