Deep oceans are not very well explored, it is possible that a relatively a few small cities can be there without human knowledge.
You will need them to deliberately avoid exploration, and you need to eliminate accidental discovery.
To keep them from exploring, have religion (e.g. they were abused by surface dwellers in the past), or some survival constraint: UV rays hurt them, they have to stay near vents that provide them with some essential nutrient.
It would help if they are in the deep ocean, so they are far from shores, and cannot be accidentally discovered by fishermen or divers.
You also want both their bodies and their artifacts to sink to the bottom rather than float up. Giant squid were discovered mainly b/c they float up when they die.
In fact, make their materials and technology biologic in nature, so they rot soon after being discarded. This way you cannot have a stray fish swallow some broken or loose piece, and later turn up in a fisherman's net.
8I feel like I must recommend Jules Verne’s Journey to the Centre of the Earth – Dubukay – 2018-11-01T14:48:55.470
8Check out the book Artemis Fowl for exactly that idea. – Aethenosity – 2018-11-01T18:09:38.987
It is encouraged for posters to wait 24 hours before accepting an answer so as to allow more answers to be posted. – Tracy Cramer – 2018-11-01T23:59:12.210