Dana 60 S60 or Ford 9"
I would like to make a point. The original 9" was not a world beater. The majority were open, if it did have a limited slip, it was weak, the 28 spline axles were smaller and weaker than 30 spline 8 3/4 axles, and the gray iron center section was very breakable.
Now there were 31 spline, nodular centers, with better "posi"s in them (sometimes detroit lockers!) but they were much less common, thats why they were expensive.
I think the average dana 60 in a mopar was probably twice as strong as the average, stress average, 9".
Now however, as a result of nascar use, gear selection is probably twice as good as a dana. There are now countless ways to make a 9 stronger than a dana (10 and 11" gear sets, fab housings, floaters, big axles, etc.) They just cost BIG bucks compared to a dana. For the big power cars (o.p's 1000hp qualifies imho) i doubt there is a single factory ford part in any of them.
Now for my worthless opinion. I have a factory dana car, an 8 3/4 in a bracket car, a nine under a tube car,and under a back half.
When i upgrade my 8 3/4, for 650-700 hp, i will get a Strange dana. The mopar guys i might want to sell to some day will prefer it.
For a 1000hp car, i would want to see a well built nine, but a 60 that gets the job done wouldnt bother me. I think it is up to the o.p. to decide, i think either can work.
Edit : one last note; if the op narrows a truck dana 60, they come with thicker (heavier too!) axle tubes. Less likely to deflect under power.