I disagree. If Apple is paying $60 a square foot (which is unheard of for prime Manhattan retail space) and the previous restaurant was only paying $15 a square foot, then that was a crime as well and should have been investigated. $15 (if real) is so incredibly low, it has to make me wonder if there wasn't some payoff involved. But $60 a square foot is incredibly low and is definitely worth an investigation. I find it easy to believe that other retailers wouldn't have wanted to pay $5 million to the restaurant to buy them out of their lease, but there would be plenty who would be willing to pay far more than $60/sq ft.
Income from rental property is not the same as raising taxes. That is prime real-estate and Apple should be paying market rate (or close to it). Every penny the MTA takes in rental income offsets future costs and fare increases. That income should be maximized, otherwise taxpayers and commuters are in essence, subsidizing the Apple store. I like Apple, but the only way I want to subsidize them is by buying their products.
Furthermore, I wonder what kind of signage there's going to be up there because after the Terminal was renovated, the policy was there was to be no advertising in the main hall. Kodak used to have a giant mural on that side of the terminal and it was taken down during the restoration for that reason. I wonder if Apple gets to violate that.