From a disease resistance standpoint, I haven't planted either. Susceptible to scab, fireblight, and cedar/juniper rusts. I'd choose something else with better disease resistance.
If those were my only choice...I'd probably go with golden delicious. There are a lot of Fuji sports/strains that vary in ripening time. I'd pick the GD to be more sure I'd have apples into archery season. An early Fuji strain might have dropped by the end of September.
What criteria do you value?