Apps referenced are for Android, and links will take you to the Google Play store.
- First, the item not specific to Boston: Shuttles operated by many universities and hospitals across the country are tracked by the TransLoc Rider app. I used this one both in Atlanta (Emory) and here in Boston (LMA/Harvard), and the real-time location data was helpful with knowing when to leave to catch the bus I needed. To find out if they have a system near you, check out their map or agency list.
- For commuter rail in Boston, the website MBTAtrains.com is the best of several tools I tried. The only feature that is missing there is upcoming departures of inbound trains. If that is something you need, this rail tracker app is the best alternative. I should also note that trains with missing location feeds appear in the app, but are absent on the website (with a notification at the bottom that the data is missing). Even so, the website's map makes it much more useful than the app. And, unless you have a monthly pass, you probably want to use the official mTicket app to buy commuter rail tickets.
- For the city buses, I recommend BostonBusMap. This app is the best of several that I tried. There is a bit of a learning curve to figure out how to navigate the many options and views, but after that it is intuitive and full-featured. I tend to use "stops and predictions on all routes" as my default view and select the stop near me--especially since multiple routes serve my usual stops.
- I haven't had much occasion to use any of the subway lines, so no recommendations on that front at the moment. Sorry.