Hewitt won 2 slams in 2001-2002 and had a nice long consistent run at #1. .. didn't win any in 2004-2005. I'll take 01-02
Hewitt was one of those guys with a certain game where he is going to be at his absolute peak during his teenage/very early 20s because he relied so much on speed and counter-attack-abilities. After a few years of playing like that fatigue/injuries hit pretty fast.
He was still very good in 04-05 (Maybe feel this was his peak) but just not as deadly as he was 01-02 IMO.
I thought by 2003, Hewitt was already beginning to lose that speed
Hewitt's best ever run of form was around Wimbledon 04 to IW 05. He was at his most consistent in the slams in 04-05 - losing only to the eventual winner every time and to Federer 5x. On the general tour e.g. below slam level he was a bit better in 01-02. He began having surgeries in 2005 which took their toll on him, he played a lighter schedule in 2005. But his play in the same was still really high.
I think in peak playing level he was probably pretty similar in both periods, but he was more consistent in 2004-2005, particularly in slams. So I would say 2004-2005 was better overall. Obviously not in achievements since Federer is a superior player and an awful match up for Hewitt, who also developed a mental edge over Hewitt after a few wins in a row.