After spending two hours fucking with pushing my reset-button and clicking upload in both ReplicatorG and Makerware, I figured out how to do it from the command line. The command line was determined from running ReplicatorG on the console and trying to upgrade the firmware.
Download and install it from http://www.makerbot.com/sailfish/install/
wget http://firmware.makerbot.com/firmware/MB-mb24-2560-Sailfish-v4.4-r1029.hex
/Applications/ReplicatorG.app/Contents/Resources/tools/avrdude -C/Applications/ReplicatorG.app/Contents/Resources/tools/avrdude.conf -c stk500v2 -P /dev/tty.usbmodem1421 -b115200 -D -Uflash:w:MB-mb24-2560-Sailfish-v4.4-r1029.hex:i -pm2560
Here's what the output said:
avrdude: stk500v2_ReceiveMessage(): timeout
<< then i pushed reset >>
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.01s
avrdude: Device signature = 0x1e9801
avrdude: reading input file "MB-mb24-2560-Sailfish-v4.4-r1029.hex"
avrdude: writing flash (132694 bytes):
Writing | ################################################## | 100% 19.12s
avrdude: 132694 bytes of flash written
avrdude: verifying flash memory against MB-mb24-2560-Sailfish-v4.4-r1029.hex:
avrdude: load data flash data from input file MB-mb24-2560-Sailfish-v4.4-r1029.hex:
avrdude: input file MB-mb24-2560-Sailfish-v4.4-r1029.hex contains 132694 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 14.68s
avrdude: verifying ...
avrdude: 132694 bytes of flash verified
avrdude: safemode: Fuses OK
avrdude done. Thank you.