Flagstaff can get feet of snow. If you check weather.com and find feet of snow, avoid both routes. At least check them. You might be best off taking I25 south to I10, and going the really long way around, especially if you wanted to see Tucson anyway.
It all depends on the snow depth. If you don't mind a little snow, then any route will be fine. If the weather is clear, then either route will be fine. If there is snow in Flagstaff, check Payson, and it might have much less. Also check going to I10, it might be totally clear, as the highest elevations are
around 5,500' but near the Mexico border, so much further south.
Have fun!
Fred.