Assuming hp is the same...
Skyline easily outhandles Supra. Skyline easily out-launches Supra.
However...
Supra easily out-accelerates Skyline once it is above about 60km/h.
If you want to do the drag strip thing, it's a hard question. You can get a GTR into the 10's without changing the internals of the engine. You can also do the same for a Supra, though you require much more hp to make up for the lacklustre launching that Supras have.
If you like to race people on the freeway, a single turbo Supra on stock internals with high octance race fuel is virtually unbeatable, and very streetable too (can just turn down boost to run 98octane for normal driving). However if you like stoplight racing, the Skyline's AWD will pretty much own the Supra.
Around a racing circuit the Skyline wins easily, Supra really can't compare.
So it depends on what you want to use them for. If you love freeway roll-ons, and have the above-mentioned single turbo (ie T88) Supra, it would require an absolutely mind-blowingly engineered, and priced, Skyline to just keep up because they have to rebuild the engine from the bottom up, and will most likely have to deal with being at least 200cc's down (unless they get the OS-Giken 3-litre block). From a stop though, the Skyline can hold it's own, and will be many seconds per lap ahead on the track, and almost always ahead on the drag strip given hp is the same.