MCU near sensors or on external board
Issues regarding option 1, in case you've not considered them yet: 


The biggest issues I think would be interference/noise/reflections on the cabling. You could end up with some very squiffy readings unless you ensure proper isolation/filtering (depending on the signals).
The extra cabling increases both the BOM cost and the production time/cost. 


My personal view would be that it need only be the communications (and power?) cabling between the main device and the sensor box. This way, you make the sensor box functionally independent and more importantly - completely replaceable. 

With a bootloader on the MCU, you should even be able to reprogram it via the comms link.

If you can't get a bootloader though, then the next best alternative would be to have an externally-accessible header on the sensor box.