The solution is to write a '1' to the digital pin you want to read; this will turn on the pullup resistor. This struck me as counterintuitive, but even though the pin is in INPUT mode, you can still write to it to manipulate the pullup. Note that this is not just a Firmata thing, but is actually available in the Arduino language as well as described
here (even though they say it's a "prior to Arduino 1.0.1" thing, I just tested it under 1.6.5 and it seems to work fine). So in Pduino you would set your pin (say, pin 5)
to input mode, then send a message 'digital 5 1' to the 'arduino' object. That should do the trick.