In a medieval society, all land belongs to the crown, and thus can't really be bought by common folk. I don't know about Waterdeep/Realms politics, though, so this may not be the case.
A quick glance through the "lots for sale" and "homes for sale" in the classifieds of today's paper makes me think that city land is worth about 10%-30% of the value of the home sitting on it, assuming a normal plot of land (less than an acre for a single-family home). My last appraisal made my lot (about 1/3 acre in suburban Minneapolis) about 18% of the total value of lot+house.
Of course, in the modern world, "suburban" land is worth more than inner-city land. People prefer big lots and natural surroundings, not crowded high-rise living.
In a medieval world, this might be backwards; the additional protection provided by being nearer the center of the city might have an effect on price. (Though the amount of magic in the Realms means any realistic attack on Waterdeep won't be a "storm the gates with a zillion soldiers" kind.) And, as always, "location location location". Being close to a river, well, guardhouse, city gate, park, etc etc, will have an effect on the price of land.
Also, most pictures and descriptions I've seen of medieval towns have the buildings right next to each other, with very little space around them. Built like that, there would be two-to-three homes on my lot.
So, as a first-order approximation, I'd say that land is worth a minimum of 10% of the value of the building on it, if it's a typical medieval town situation where there's no "yard" around a house. Accepting the DMG prices, this means a lower-class "simple house" is really a 900gp building on 100gp of land.
I would just scale up from that figure; middle-class or upper-class areas would be 200gp or 300gp for an equivalent-sized plot, or more for land in a prime location. A middle-class 'grand house' probably needs 2 to 4 times the area of a simple one, and probably will have a small yard or courtyard equal to another plot, so land for a grand house should be worth 600-1000 gp. An upper-class mansion--with a stable, servants' quarters, guest house, and garden, in addition to some open area--might sit on grounds 20 to 60 times the size of a simple house, costing 6000-18000 gp.