Federer would stil be dominant even if he played in the 90's.
He'd probably have a little less than 17, but he'd still lead in the Slam count.
His main roadblock would be Sampras obviously, but even at his peak Pete never had the consistency to rack up single-digit loss seasons or 90-95% annual winning percentages. His game didn't really allow for that kind of sustained dominance. But Roger's game does.
He'd probably win less Wimbledons because of Sampras, but he'd probably compensate for that by winning more than 1 FO (assuming prime Rafa also didn't get wormholed back to 90's) and more AO's.
I've also a suspicion his game would've been even BETTER if he developed in the 90's. We saw a glimpse of that in 2005 version of Fed, where he already had that superior baseline game but could STILL S&V. 90's Fed would've developed a SUPERB net game to compliment his dominant backcourt game.