MakerBot Industries

If you move the Y axis by hand do the LEDs blink on the steeper board? If they do not, the board is not being powered. On a TOM 5V power comes from both the USB connection to the computer and it's own supply. If they light up then 5v is good. If they do not 5V is not reaching the stepper. Check the connections carefully (this advice is valid for any issue).

If they light up and you still see no response by the motor the. 12V is gone. Same approach and check connections.

Still no life, connect the y axis to another stepper and check if that stepper works. If it does put everything back as it was and if the problem persists you may have a dead stepper board. Sometimes the changing of the cables solves some contact issues too.