I believe making the most out of quantum shielding is the key to beating Grey Knights.
GKs are fearsome in ranged anti-infantry and close combat anti infantry. However, their arsenal of long range AT weaponry is limited to a few costly vehicles of their own.
In light of this, your Necrons will be a lot safer in ghost arks than in the open. And since it is objective games you are talking about, you want to combat the Necrons' second major flaw by using transports: lack of mobility.
Doomsday Arks are awesome. All you need to make sure is give them a good LoS during deployment and their great range can create large sections of the table under "area of denial" status.
As for independant characters....I don't have the codices at hand, but I think GKs can make heavy use of deepstriking. I think Imotekh has an ability to make deepstriking troops have a hard time, and I believe Crypteks can do this, too, but I'm not sure. Load up on them.
Necrons also have this dude who can take control of enemy vehicles...if you have spare points left over, take him, too. So fun to see that fancy, shiny Dreadknight turn on its own brethren.
And whatever you do, do NOT use C'tan. They're a waste of points against GKs, as the GKs are tailored to slaughter powerful ICs of other armies. Regarding this you might wanna put Imotekh in a barge.