How can I connect Puck2.js to PN532 NFC/RFID ?

What you're doing sounds good. You could try software I2C just in case?

var i2c = new I2C();
i2c.setup({scl:D28, sda:D29});
var nfc = require("PN532").connect(i2c);

That'll be able to use the internal pullup resistors which may work if the PN532 doesn't have any.

Another issue could be the voltage. IIRC the PN532 needs quite a bit of power to get its coils working - it's possible that the 3v CR2032 doesn't supply enough power.

In that case, you'd just have to:

• Leave the VCCs connected
  
• remove the CR2032
  
• add an external 3.3v supply to VCC