Don Chiofaro has notified City Hall that his company would like to build two towers, with a combined 1.5 million square feet of mixed-use space, on the site of the Harbor Garage in downtown Boston.

The Chiofaro Co. proposes to replace the seven-story, 1,380-car garage with 860,000 square feet of office space, 220,000 square feet of residential space, 70,000 square feet of retail space and a 350,000-square-foot hotel. The project would be spread over a combined hotel/residential tower and an office tower, and include restaurants, retail, and a market on the ground floors, with parking and service docks below grade, according to a letter of intent filed with the Boston Redevelopment Authority.

Chiofaro estimated the cost of the project at $900 million. He said the amount of equity his firm and their partner, Prudential Insurance Co., needs will likely depend on the strength of pre-leasing.

“It’s the best site in the city,” Chiofaro said. Because of that, when his company purchased the garage at 70 East India Row, across from the Rose Kennedy Greenway, last year for more than $150 million, “We made up our minds that we were going to outbid everybody.”

“It arguably has two front doors, and both are fantastic,” said Ted Otis, a Chiofaro Co. executive.

Chiofaro added, “Now’s a good time to get queued up and get approved. When [the economy] turns, we’ll be the first one out of the chute, rather than the last. It’s very hard to be the first, because you’ve got to make people believe you – that things will get better. But if you’re the last out of the chute, you might as well wear a black suit, because you’re going to your own funeral.”

The developer has not specified how tall the two planned towers would be, but he allows that the project will need variances for height and floor area ratio. Descriptions of the project’s earlier incarnations put its height between 40-85 stories, making it higher than the neighboring Harbor Towers. Harbor Towers was originally envisioned as a three-tower complex, though only two were built.

The letter of intent predicts the generation of $30 million in new tax revenue, promising to bring “new vibrancy and much needed retail” to the waterfront. Chiofaro said the project may also create up to 4,000 construction jobs.

The towers will face each other, separated by indoor public space that provides sightlines between the Rose Kennedy Greenway and the harbor. The opening will be wider than the 100-foot-wide archway at nearby Rowe’s Wharf. The design, Chiofaro said, will “create access to the water from a variety of different locations” and “take down the wall that is the garage.” Chiofaro has not released renderings of the project.

Harbor Towers’ 1,200 residents park in the garage. They’re legally entitled to 624 spaces, though residents currently utilize around 300. Chiofaro said that parking for residents of Harbor Towers will be “provided at all times,” and that his company has a “moral obligation” to provide public parking for the nearby New England Aquarium. The garage will come down in phases, so that it remains operational while construction on the new, underground parking structure proceeds. Chiofaro plans to open the entire new sub-surface parking before vertical construction on the towers is complete.

Suzanne Lavoie, a former Harbor Towers trustee, said that Chiofaro approached the towers’ board after buying the garage, but thus far, the developer hasn’t specified where residents will park during, or after, construction. “That’s definitely a concern. And construction is a concern. We’ve lived through the Big Dig and a $75.6 million internal renovation. Now there’s going to be construction next door?”

Lavoie added, “He’s trying. I give him that. It is a challenge. How do you put 1.5 million square feet on that plot? You’ve got two choices – go up or down. We are a residential community in the city. We understand the area will evolve and develop, and we’re not opposed to that. We do want development that will be considerate of us as neighbors. The question is, what will he put on the site, and is it something Harbor Towers residents can feel comfortable with? You can’t hide a 50-story tower.”

Building orientation has the potential to become a flashpoint. Harbor Towers residents pay condo fees based on their height and views. That fee system was established in the early 1980s, when southerly-facing units had little to look at. There’s a fear that the orientation of Chiofaro’s towers may wall off the views of up to a third of the towers’ residents – a good portion of whom are already paying higher condo fees than their neighbors. In a building complex that just emerged from a bitter internal political battle, a war over views and condo fees won’t be a welcome one.

Administration officials had no immediate comment on Chiofaro’s plans.