I was there 10 years ago, but still hope to return to the same hotel I stayed in on Santorini, in Thira, called Enigma. Don't let the cheesy name deter you - it was incredibly beautiful, with rooms carved into the mountain, very reasonable, wonderful owners. Hope it's still there.
Day out with Thomas is a zoo - and I think the place is better on a non-Thomas day. In addition to the Strasburg Railroad, there is a ton of train related things - we really loved the Pennsylvania Railroad Museum and the Toy Train museum there. We stayed a bit farther away in the Hotel Hershey, which is just a nice hotel with a great restaurant for brunch. If the kids want something interesting and a bit of a novelty, there is the caboose hotel there (Red Caboose Inn? Can't remember the name) - all the rooms are old cabooses refitted. I think a couple of them are large enough for a family of 4.