Other option is Grand Cozumel Diving. Located downtown on the 5th Avenue.
They have a promotion right now $535us/person for 5 days of diving and accommodation.
They have a really nice boat, the Anita. With bathroom and sun deck. It's big but they do small groups of usually 3-4 divers. They also let you do long dives (60-70+ min). Lunch is served on board with. Great atmosphere on the boat. Trilingual instructors (French/English/Spanish)
The rooms are also quite nice, king size beds, with AC, WiFi, private bathroom, access to a kitchen and to the backyard with pool. It's not an hotel and it's not on the beauch though, it's more like a BnB type of place. It's also really well located close to all amenities.
There not really well known yet because they use to have their diveshop a bit far from downtown but they've been on the island for 8 years. They opened their new shop downtown last year.