What are the best places to stay in Santa Fe with a 5 and 2 year old?
I don't know if it's the best because I don't have children, but I think the Hilton Santa Fe Historic Plaza would be a good one. Since it's not a B&B, I feel it would work, plus it is very nice and not too far from the main areas. (And a short walk to Cafe Pasqual's, my favorite place to eat in Santa Fe.)
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I would recommend
Close to Ski Santa Fe Your accommodations at Villa de Santa Fe will be comfortable and roomy, with disabled access rooms available. You will even have kitchen facilities, complete with a two burner stove top, toaster, refrigerator, microwave, and even a dishwasher. You will feel just like you are at home when you stay at Villas de Santa Fe.