The short answer
For a first desert trip, Merzouga. Its Erg Chebbi dunes rise to around 150 m, the road is paved to the sand and the choice of camps is wide. Zagora is closer to Marrakech, about 6 hours of driving, but the dunes near it are much smaller. Its real prize is the route on to Erg Chigaga.
In more detail
Erg Chebbi is the desert from the photographs: about 22 km of orange dunes beside the village of Merzouga, visible from far off. It is busy in season, with many camps along the edge, but it is easy to reach and the sand is the real thing.
Zagora is a palm oasis town in the Draa valley, Morocco's longest river valley, and the road there through Agdz is one of the prettiest in the south. The dunes close to town are modest, and first-timers who have seen pictures of Erg Chebbi can come away underwhelmed. Zagora makes sense when time is short, or as a stop on the way to M'Hamid and Erg Chigaga, which is wilder and quieter than Merzouga but needs a 4x4 over piste.
So the choice is scale and ease against solitude and effort. Families and older travellers usually do better at Merzouga. Travellers who have already seen Erg Chebbi, or want the emptiest dunes, do better with Zagora and Chigaga. A long loop can include both.