Upload & Sell: On
I'd be leaning toward the low-mileage unit. There are other moving parts and areas of wear and abrasion that affect the functioning. Small things matter too -- like the viewfinder rubber eye piece, battery(ies), etc.
If and when the shutter needs replacing, it's not disastrously expensive, and then you'd have an even newer-newer camera than one with a new shutter and 200k (or whatever number) actuations.
Now, if the unit with the new shutter has under 100k total on the body, I'd go with that! That's still a pretty fresh piece.
I bought a 1D2 with 115k actuations, and was on its second shutter, from about 40k on. It had some problem or needed clean/check, and CPS replaced the shutter for me at no charge (thank you, Canon!), and I shot it for about 20k before selling. That was a very nice camera and I'd have no regret buying it again.
You really need to examine them and talk to the owner to make your decision. Either one may still need a trip to Canon due to occasional AF hiccups, so keep that in mind with the 1D3 model -- usually it's free, if a problem is found.