City Quays is an office-led development on the east bank of the Lagan, close to the city centre.
The application states that the nine-storey hotel would be "upper midscale" in terms of market position.
It adds that a new public space, to be known as Waterfront Square, would be created as part of the development.
The first City Quays office has been completed and is largely occupied by the law firm Baker and McKenzie.
Work is beginning on a second office and further applications are due to follow.
The hotel plans will now be considered by Belfast City Council's planning committee.
Belfast Harbour has filed a planning application for a 190-bedroom hotel at the City Quays development.