I have no idea. That's a really tough question.
Probably the best fast bowling pair I saw, at their peak, were Ambrose and Walsh in 1999. The West Indies basically drew that series because their three best players played out of their skin, and walked off as skeletal champions.
Lillee and Thompson would never be my pick. They had an awesome peak, but it lasted two seasons really. I've seen highlights of the 74/75 Ashes series and the 75/76 West Indian series and they look amazing. But Australia soon became a side that relied heavily, and I mean heavily, on Dennis Lillee.
Waqar and Wasim? Best ODI opening pair, but best Test pair? They'd be up there of course. They were probably my favourite pair to watch. I used to try and mimick Waqar's actions. Like always, the ball never swung with me.
I wish I'd seen more of Holding and Marshall. It wouldn't surprise me if they were the best. The funny thing about them is they might be underrated because they blended in with Garner and Roberts etc.
McGrath and Gillespie are underrated. They're not close to being my pick, but I always felt Gillespie was an underrated foil to McGrath. My memory has been failing me recently, but I do distinctly remember a bowling spell with McGrath and Gillespie from 2004 against India. I forget which Test it was. But Tendulkar and Dravid were batting, and as good as any two batsmen in the world back then. McGrath and Gillespie kept them down to about 20 runs off 100 balls before someone went out. The pitch wasn't offering either of them much, but they just kept it tight and kept the pressure on.
I kind of felt bad for Gillespie and how he fell apart in 2005. Gillespie was underrated, and far better than a lot of the overrated Aussie fast bowlers from the 90s (Reiffel etc).