One strategy would be to estimate the benefits to subway riders, the benefits to drivers (who face less congestion), the benefits to businesses (which enjoy a deeper labor pool and increased productivity), the benefits to retailers (which enjoy a larger market), etc., and add them up. I don't know how to do that.
But another strategy is to estimate the subway's impact on property values. After all, the value of the subway ought to be capitalized into property values. (Randal O'Toole agrees, but inexplicably refuses to reckon this a positive.) Real property in Manhattan is very expensive in part because of its density of residents and employees. Real property elsewhere in the city and the metropolitan area is very expensive in part because residents there are close to -- and can get to -- Manhattan. Without the subway and commuter rails, Manhattan's density would be impossible, and residents in the metropolitan area would have a harder time getting to it, assuming they'd still want to.
This estimate, too, is beyond my capability, but at least I can estimate the value of New York City property to one order of magnitude. In 2008, the assessed value of all real property in New York City was $800 billion. (The market value surely was higher.) Estimating the value of the property elsewhere in the metropolitan area is a lot trickier. But because New York City has only 42.5% of the metropolitan area population and just 4.5% of the metropolitan area's land area (Wikipedia), it's a safe bet that the rest of the metropolitan area was worth at least as much in 2008, for a total of $1.6 trillion. Since property values have declined sharply in the metropolitan area over the last year, let's discount this by 25% to $1.2 trillion.
The value of the subway and commuter lines to New Yorkers is the difference between the value of the metropolitan area property with and without the subway/commuter lines. (Consumer surplus will increase the total, but I ignore it for convenience.) The subway and commuter lines are, conservatively, worth at least $12 billion per percentage point in difference.
I can only make a wild guess about the magnitude of the difference. We do know, though, that Manhattan's density would have to drop sharply without the subway. Manhattan's standard density is more than 70,000 ppsm. New York City's standard density is 26,000 ppsm. Among large American cities, San Francisco's is next, at 17,000 ppsm. And San Francisco is quite compact for an American city; it's just twice the size of Manhattan. Chicago, 25% smaller than New York City (and blessed with the "L"), has a density just half of New York City's. I don't see how Manhattan could sustain a density more than quadruple San Francisco's, nor do I see how New York City could sustain a density more than twice Chicago's. In other words, I think it's likely that Manhattan and New York City would lose half their population; Manhattan surely would lose more than half its daytime work force.
My wild guess is that New York City proper would lose a large percentage of its value and the metropolitan area a similar percentage. 20%? 30%? These numbers seem extremely conservative to me. And that puts the total value of the subway and commuter rail to New Yorkers at a rock-bottom minimum of $240 billion.
One check on this would be to look at the cost of a disruption in service. During the 2005 strike, the city estimated each day of disruption after the first cost the city $300 million. If we annualize that loss (ignoring weekends) and capitalize it using a 10% discount rate, the total value of the subway (and just the subway) is $795 billion. The long-term loss would be lower as residents adjusted (by switching to buses, say), but it's hard to see how the long-term loss would fall by more than two-thirds. (And, remember, we've ignored weekends.)
My $240 billion estimate, while just a guess, seems a reasonable guess. And it seems very reasonable to assume that the value falls somewhere within the range of $100 billion to $500 billion.