Cottee felt the Academy pair were outstanding for their promotion campaign.
He told West Ham TV: "Mark Noble won the Hammer of the Year and has done really, really well. But for me my Hammer of the Year was James Tomkins. I think it was very close between them and I'm really pleased Mark won it but James was outstanding last season.
"Tonks was our Man of the Match at Wembley and should push on next season into a top, top defender."