By some measures, the Valley Transportation Authority and Caltrain are among the most troubled transit agencies in the nation. But a report released Wednesday by the Brookings Institution ranks transit in the South Bay as the second best in the U.S. at linking where people live with where they work.

“Ranks second?” said transit consultant Tom Rubin, a longtime VTA critic. “How many did they rank — two?”

Actually, they ranked 371 transit operators in 100 metropolitan areas, and the South Bay fared better than every one except Honolulu.

This is the first nationwide study of its kind on how many people live within three-fourths of a mile of a bus or train stop and can get to work in up to 90 minutes on public transit. It’s a counterintuitive finding, as you might think larger, older Eastern cities have the most residents who are within walking distance of a quick bus or train ride to their place of employment.

The West makes a strong showing in the report, with 15 of the top 20 agencies, including the San Francisco-Oakland-Fremont corridor at No. 16. Denver, Las Vegas and even Modesto and Bakersfield all made the top 20, with Los Angeles and San Diego just missing at No. 24 and No. 25.

“This isn’t about how well the system performs, but what they are capable of,” said Alan Berube, one of the study’s authors. “It may be surprising to many people.”

That it is, especially the lofty spot held by the VTA and Caltrain.

Rubin called the ranking “incomprehensible,” saying, “I believe anyone who has studied the subject would have great problems figuring out how such a result could be achieved.”

In the San Jose area, 96 percent of workers live near a transit stop, compared with the national average of 69 percent. And 58 percent of all jobs are reachable within 90 minutes, compared with 30 percent across the country. In the San Francisco-Oakland-Fremont area, it’s 92 percent and 35 percent.

By comparison, the figures for the New York-to-Long Island area are 90 percent and 37 percent.

The West’s dominance reflects the changing American commute, Berube said. Where once the vast majority of workers lived either in a big city or close by in the suburbs and worked downtown, 39 percent now commute from one suburb to another.

Older transit systems in Boston and Chicago built before World War I resemble a bicycle spoke, with train lines feeding into the center of their downtowns, while more people are working elsewhere today.

But in the West, transit lines were often started in the 1960s and were designed to deal with the exodus to outlying cities like Campbell and Mountain View in the South Bay, and Livermore and Walnut Creek in the East Bay.

“Geography is also a key,” Berube said. “In the West, you have mountains. Like on the 101 and 280 corridor in the San Jose-to-San Francisco area. People are more limited as to where they can live than in the South, where farmland rolls on forever.”

Plus, states like California have approved global emission standards that put an emphasis on getting people out of their cars. That’s why development is focused on the light-rail line along First Street and Tasman Drive in North San Jose, and in Peninsula cities like San Carlos and San Mateo along the Caltrain tracks.

“The report focused on the availability of transit, working-age population and total jobs,” VTA General Manager Michael Burns said. “I’m not surprised that we fare well when these are the inputs. Our area has a large number of working-age folks and our primary market is travel to work.”

That is why Lisa Bonetti takes the 101 express bus up to four times a week from her home in Sunnyvale to Palo Alto, where she works at Communications and Power Industries as an engineering manager.

“I take the bus for reasons of economy, efficiency,” she said. “I can read and answer emails on my smartphone and it makes me feel like I’m contributing in a small way to improving the Bay Area air quality.”

Yet the VTA has one of the nation’s lowest farebox recovery rates, the percentage of operating costs covered by fares, at 14 percent. While it has balanced its budget and been able to hold fares at current rates and avoid service cuts, attracting more riders has been difficult.

And Caltrain was rescued from near-financial collapse last month, when it faced a $30 million deficit.

Now the challenge for both is to attract enough riders to live up to their Brookings ranking.

Contact Gary Richards at 408-920-5335.