Dismantling the LMDC, for which he appoints half the board members, would "eliminate one redundant layer of bureaucracy" that has stalled rebuilding of the site, he said in the op-ed.
He said that a commuter rail hub under construction at ground zero, particularly an underground mezzanine hall that overlaps with the Sept. 11 memorial, "is too complicated to build" and should be changed.
The mayor, who spearheaded $350 million in private fundraising to build the memorial, also said the agency that owns ground zero should commit to opening the memorial to the public by the attacks' 10th anniversary, in 2011.
The city has long sparred with state development officials, a private developer and the Port Authority of New York and New Jersey, an agency controlled by two governors, for greater authority over what is built and how quickly at ground zero.
A recent agreement gave the city police department control over security at the site, and city streets will eventually run through the rebuilt 16-acre site. The Port Authority and developer Larry Silverstein are in charge of building five office towers, the memorial and the transit hub.
Gov. David Paterson this summer ordered the agency to reevaluate all the ground zero projects, which the agency has said are all over budget and behind schedule. A report is due at the end of the month.
Paterson on Wednesday called Bloomberg's remarks "an important contribution to our ongoing dialogue, reminding us that serious issues need to be addressed to complete the rebuilding our nation deserves."
He said he hoped the memorial could be built by Sept. 11, 2011, but didn't comment on whether Spanish architect Santiago Calatrava's hub would be dramatically scaled back or whether he would abolish the LMDC.
The Calatrava hub has become one of the biggest obstacles to rebuilding quickly at the site because of underground terminals and connections that directly affect the schedules of the memorial and three other office towers.
The $2.5 billion project's cost was at least $1 billion over budget; delays in the hub affect the memorial, which has one corner of its tree-covered plaza surrounding two reflecting pools built directly over the hub.
Bloomberg said later Wednesday that Calatrava designed a "magnificent" building.
"It just may be that the economics of it in this day and age don't work," he said.
Calatrava's office declined comment.
The LMDC, formed by former Gov. George Pataki and former Mayor Rudy Giuliani just after the 2001 attacks, announced it was going out of business at the end of Pataki's administration, existing only on paper so that federal rebuilding funds could be distributed.
Eliot Spitzer, who called the agency "an abject failure" before he became governor, changed his mind and decided to resurrect it, appointing one of his chief aides to chair it.
The agency still distributes funds to downtown projects besides ground zero but spends most of its time overseeing the dismantling of a toxic skyscraper where two firefighters died a year ago.
"They didn't have to create it," the mayor said of the LMDC Wednesday. "We did not need another level of authority."
A Lower Manhattan Development Corp. spokesman declined comment.
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