It takes a prospective visitor to tell someone that lives here about something....I know where Vathipetra is, and have driven through it, but didn't know there was anything there to see!!! Whatever it is, it is not marked on any of my maps.....
Most of the smaller archaeological sites close at 3pm. Knossos is about the only one that stays open late. I think that Knossos is enough archaeology for one day.
There are lots of wineries on Crete, in fact I really do not know why someone has not had the idea of starting wine tours. One of the best known is Boutari at Skalani (Boutari actually have wineries all over Greece), They do have a restaurant there too, but be warned that the last time I went there it was not cheap!
There are others centred around Arkaloxori too... Do a Google for 'arkalochori wines'. You will find places to eat there too. Just look for the 'brown signs' as you are driving to find the wineries.
My favourite winery is down near Moires near the south coast which is a bit out of the way for you on a one day trip. A friend of mine has grapes down that way too.There is a special grape grown here too which is accustomed to growing at high altitudes, it makes an excellent red.
On your return trip to Heraklion, pass through Thrapsano, a village renowned since Roman times for its pottery, and then via Kastelli, which is a busy hill 'town' with a military airport, to the coast. If you look closely you can see the remains of the Roman aqueducts that were used to bring water down to the coast.
Do bring a good map with you, the one you get with a rental car is almost useless, it makes everywhere look like it is 10 minutes drive when it is more likely to be 30 minutes, and be aware that some of the roads on your map might not have been built yet. Beware of goats too.