By the time the MCTA..forerunner of the MTA purchased the LIRR, the LIRR was nolonger a publicly traded company. By 1965, the PRR was in possession of 100% of the LIRR's stock. Since the stock was nolonger publicly traded, and the LIRR had not paid a dividend or made a profit since 1930, the stock was valueless except for the scrap value of the LIRR.
What the PRR and MCTA did, was, disregard any possibe stock value, since it had no value and instead, agreed on a sale price...$65,000,000. This price reflected the assets of the LIRR and the State's willingness to aquire a bankrupt, but very necessary, money pit. Without New York States intervention, the LIRR on asset value alone, was worth far less. Even today, the LIRR's actual value is in it's assets and the willingness of an entity to buy it regardless of the costs of running it. Without a willing entity to buy it, it has asset value only, since it costs more to operate it, than it does to simply liquidate it.
The LIRR stock certificates were transferred to the MCTA in the sale. They were in a warehouse and there was a fire which destroyed all but a few certificates and Gold Bonds. This is the reason why LIRR certificates are so rare. Surviving examples were from collections, like Dr. Ronan's (the first MCTA Chairman) and "speciman" certificates. They are quite valuable, fetching $500 to $1,000 per item.
It was a typical corporation with stock (100% owned by the MTA), until 1979. In that year, it was reincorporated as a "Public Benefit Corporation". This was done in order to solidify it's relationship to the State in hopes that the MTA/LIRR would be able to have it's employees under the NYS Taylor Law instead of the Railway Labor Act. Not only would this move have ended the ability for LIRR unions to strike, but, possibly have ended the LIRR from having to pay into Railroad Retirement, which is more expensive than Social Security. Also, the Federal Employer Liabilty Act (FELA), which is the Railroad industry's Worker's Compensation, would have been gone from the LIRR..they would simply purchase a Workers Comp policy and not had to abide by the provisions of the far more expensive FELA. Their efforts failed...the U.S. Supreme Court ruled in favor of the LIRR unions and the Federal acts are there to stay (see UTU vs. The Long Island Rail Road Co., 1982)..
Hope this helped