Using the NodeMCU (or any similar development board), the flash location is 0x0000 and the mode is dout.
esptool.py -p /dev/ttyUSB0 write_flash -fm dout 0x0000 esp8266_deauther.ino.nodemcu.bin
/dev/ttyUSB0 is the COM port of your device,
write_flash is telling the program to write to flash memory,
-fm dout is the flash mode and
esp8266_deather.ino.nodemcu.bin is the name of your .bin file.
An easy to use GUI flasher for Windows and Mac: esptool-gui.
Select the COM Port and the .bin file (firmware), then just press upload.