If powering over Vin pin is working, you can use the board without USB.
ESP8266 is bootloaded over UART pins. These are pins marked RX or D9 and TX or D10 on the NodeMcu board. You can use USB to TTL serial adapter to bootload (flash) the esp8266. To put the esp in flashing mode hold the FLASH button and click the RST button and then release the FLASH button.
You can then upload a sketch with ArduinoOTA library and do following uploads over OTA. After USB upload of a sketch, reset the board with RST button before doing the first OTA upload.