The open ideas competition organised by Arch Out Loud called for an aquarium and waterfront proposal at Long Island City's 11th Street Basin – opposite Louis Kahn's Four Freedoms Park at the lower tip of Roosevelt Island.
Lissoni came top with his Aquatrium design, comprising two circular elements within an extended basin.
The Aquarium and Marine Center would be formed from a submerged two-level island that extends into the river.
A ramp modelled on the striations of seashells would begin at the lobby entrance and lead visitors along a pathway down below water level.
"Having the water level define the starting point of the project, the site is excavated to become a spacious and innovative water basin," said Lissoni's team.
Along the route, eight bubble-like "biomes" would host sealife from four oceans, Atlantic, Pacific, Indian and Southern; and four seas, Caribbean, Mediterranean, Tasman and Red. In the centre, an iceberg represents the North and South Poles.
"The main idea is to generate an environment whereby visitors feel that they themselves are entering the water to discover the beauty of the marine life on display," the team said.
At night, a grass-topped sliding roof would cover the circular space "like a shell protecting a pearl" and create a planetarium.
The site would be enclosed by a boardwalk that wraps around the aquarium to connect the two sides, while a sloped beachfront would enclose a parking area and form a public space with panoramic view of the Manhattan skyline.
"Our project creates a dynamic system that interacts with its surroundings, offering multiple ways to experience the water world," said Lissoni's team.
Second place in the competition went to a proposal by Brooklyn architect Dominik Sigg. His Vers La Mer entry features a series of illuminated cubes connected by walkways, designed to looked like a flooded city.
"In light of rising sea levels and flooding events threatening metropoles around the world, this proposal investigates a maritime urbanism where the built fabric of the city shifts from traditional solid ground to a floating existence in harmony with the ocean," said Sigg.
Giant tanks would sit in the centre of each cube, which visitors could view from two levels. Floating platforms and planters with salt-marsh vegetation around the site would form a public water garden.
A design called Merroir by a team of professors and researchers from the US came in third place. Instead of traditional tanks, the group proposed a network of 30 pod-like chambers known as diving bells around the New York area.
At the East River hub, a below-grade trench would lead visitors past a collection of test pools to a tower that would offer views from above.
Honourable mentions were also awarded to ideas that included a grid of pylons, which would encourage the growth of coral and a series of towering glass tanks.
"The selections are focused on projects that challenge the relationship between city and waterfront, using the aquarium program as an opportunity to bring the city and its people close to the water in a new way compared to traditional parks and aquariums," said the jury.
Although none of the proposals are likely to be realised, a variety of unusual aquariums are underway around the world, such as Foster + Partners' marine science museum in Taiwan and Henning Larsen Architects's building that resembles a cluster of pebbles in Georgia.