Even if you're only going by Premier League season it still goes to Man Utd, although it would be 99/00 instead. Going through the season undefeated may be nice, but that season we ended up with more points and scoring more goals than what Arsenal did last season. It's a case of 3 wins and 1 loss will end up giving you more points than 2 wins and 2 draws, even though the second is the one who can brag about being undefeated for four games.
99/00 Man Utd - Won 28, Drew 7, Lost 3 = 91 points (scored 97 goals, conceded 45 = difference of +52)
03/04 Arsenal - Won 26, Drew 12, Lost 0 = 90 points (scored 73 goals, conceded 26 = difference of +47)
But if you're including other competitions, I'd rank them like this:
1. 98/99 Man Utd treble winners
*huge gap*
2. 99/00 Man Utd
3. 03/04 Arsenal