MTA Chairman Thomas Prendergast and AT&T New York President Marissa Shorenstein announced the winners at an awards ceremony and app demonstration in Grand Central Terminal's Vanderbilt Hall.
The grand prize for best overall app, worth $20,000, went to Citymapper, which uses real-time transit information to improve travel guides.
The second-place winner of $10,000 was Subculture.FM, which connects riders with artists seen on the subway.
Third prize and $5,000 went to Transit App, which uses real-time data to advise riders of train and bus locations, departure times and service changes.
Citymapper won an additional $2,000 as the MTA Wish List app.
Honorable mentions ($1,000) went to Accessway, a tool for the blind and visually impaired to navigate the subway system and Bus NYC, which provides live departure and arrival data for all bus routes.
Finally, the $1,000 Popular Choice Award went to Moovit, which received the most public votes for combining real-time MTA data with user-information riders can provide from their own experiences.
"The app developers who competed in this challenge have shown that they have the know-how, the enthusiasm, and the energy to do great things with the open data we and others provide," Prendergast said. "And we are glad that so many in the tech community have put their efforts into helping the MTA, and, more importantly, our customers. That's why we are going to continue to expand the amount of open data we provide."
The apps were developed as part of the 2013 App Quest virtual challenge that launched in May with a weekend hackathon - the first to be officially sponsored by the MTA. Developers had the opportunity to continue working on their apps through the final deadline in August. App Quest received 49 total submissions.
In the last year, AT&T has helped lead the activation of wireless service in underground subway stations, and the MTA's Transit Wireless program has connected 36 stations in Manhattan to free public WiFi. The MTA has announced it will expand Transit Wireless to the next 40 stations, in Queens and Manhattan, by the first quarter of 2014.