That's a tough one to call.
If you're talking about best starting XI rather than best squad then it's a different answer in my opinion.
The 98/99 team won the treble because of the squad we had (Sheringham coming off the bench in the FA Cup Final, Keane and Scholes suspended for the Champions League Final and Sheringham and Solskjaer coming off the bench to win it). Although the midfield of Beckham, Keane, Scholes and Giggs was one of the best this club has ever had.
However, the 93/94 double winning side was a fantastic starting XI. It had Cantona! And the Bruce/Pallister pairing, which was fantastic. Hughes is still one of my favourite United players, the battling midfield pairing of Keane and Ince (even if he did turn out to be a traitorous dog by joining Liverpool), the pace and skill of Kanchelskis and Giggs on the wings. What a team!
The current squad still need to prove themselves by winning back to back Prem titles, a double, treble or, dare I say it, quadruple.