But now, both museums are making big plans to rebuild their visitorship in 2012 — possibly including a joint exhibit.
Susan Henshaw Jones, who is running the Seaport Museum on an interim basis, said she is in talks with the American Folk Art Museum to mount a major exhibit at the Seaport Museum next year.
"We are very much hoping that the Museum of American Folk Art will do exhibitions in four galleries [at the Seaport Museum] starting in June," Jones said at a City Council hearing last Friday.
Jones — who is also director of the Museum of the City of New York, and is credited with turning that museum's fortunes around — said she hopes the two museums can find a way to support each other as they both recover.
"That's an institution we all want to keep in New York," she said of the American Folk Art Museum.
Jones did not say what the American Folk Art Museum, which is based at 2 Lincoln Square after giving up its much larger West 53rd Street building earlier this year, would exhibit at the Seaport Museum's Fulton Street galleries. The Folk Art museum recently mounted a major show of quilts, including a 9/11 tribute quilt.
Representatives from the American Folk Art Museum did not immediately return a request for comment.
Last Friday, Jones also updated the City Council on the Seaport Museum's future, warning that its recovery is going to be gradual.
The museum is rebuilding its membership from scratch and has a marketing budget of just $20,000 for the next year, Jones said.
Still, the museum has received donations and grants, including $2 million from the Lower Manhattan Development Corp., and has already restarted educational programs and reopened Bowne & Co. Stationers, a 19th-century print shop and exhibit.
The museum's galleries will reopen to the public Jan. 25 with exhibits of historic Seaport artifacts, along with more modern displays, including galleries showing items manufactured in New York today and photos of Occupy Wall Street. The Seaport Museum will also host the Mannahatta/Manhattan exhibit that debuted at the Museum of the City of New York in 2009, showing the island as Henry Hudson found it more than 400 years ago.
The museum will be open Wednesday to Sunday and will charge an adult admission fee of just $5, Jones said.
Jones is also overseeing repairs of some of the museum's historic ships, including the Wavertree and the Lettie G. Howard.
But the museum cannot save all of its aging vessels, so Jones is looking for a new home for the Peking, a 100-year-old merchant ship built in Hamburg, Germany. The Seaport Museum is offering to transport the Peking back to Hamburg if the city is willing to restore the boat, Jones said.
Jones will manage the Seaport Museum for one year, with a possible six-month extension, and then it is possible that the Museum of the City of New York and the Seaport Museum will merge permanently.
In order for that to happen, Jones said she will need to prove that the Seaport Museum can sustain itself on a $3 million annual budget, far less than the $5 million or more a year that the museum's prior leadership was spending.
Councilman James Van Bramer, who chairs the Council's Cultural Affairs Committee, told Jones at the hearing that he was glad to see her at the museum's helm.
"You're doing an amazing thing for the city of New York to take this on," Van Bramer said. "You've stepped up to the plate."