They are two archipelagos in the same national park, with the same permit rules and less than an hour away by boat. Quick answer: Cíes has the more famous beach; Ons has fewer people and is still inhabited.
Cíes Islands
Ons island
Facing
the ría de Vigo
the ría de Pontevedra
Area
3.091 ha (433 land)
2.641 ha (470 land)
Daily quota (summer)
1.600-1.800
1.300
Daily quota (winter)
250-450
250-450
Usual departure ports
Vigo, Cangas and Baiona
Bueu, Sanxenxo and Portonovo
Inhabited?
No (ruins of the old settlement remain)
Yes, still
Campsite
Yes
Yes
Permit
Same Xunta website, same dates, same rules
Choose the Cíes if…
You are here for Rodas beach: it is the northwest's postcard and Ons has no equivalent.
You want cliffs over 150 metres and a lighthouse walk over the open ocean.
You are leaving from Vigo, Cangas or Baiona, or want the widest choice of sailings (Vigo runs up to ten a day).
Choose Ons if…
The Cíes are sold out on your dates: Ons has its own quota and less demand pressure.
You are drawn to the human side: Ons is still inhabited and keeps an ethnographic heritage the Cíes no longer have.
You fancy something different: sea caves such as Buraco do Inferno and the Melide dunes.
You are staying on the ría de Pontevedra: from Bueu, Sanxenxo or Portonovo it is right there.
The mistake to avoid: assuming that if the Cíes are full you can just turn up at Ons. It also needs a prior Xunta permit in high season, requested on the same website (choosing "Isla de Ons" instead of "Islas Cíes").