I have 2004 Agassi as a better HC player than 2011 Nadal and the results back up my statement.
I wasn't particularly sure about this so I pulled up the big events for a comparison:
AO: This one goes to Agassi for sure. Nadal bowed out rather meekly to Ferrer in the QF while Agassi played and lost one of the best matches I've seen at the AO (at least for the first half) against a zoning Safin in the SFs.
IW: This might be even. Both guys lost to the eventual champion in deciding sets (Nadal did so in the final while Agassi drew Fed in the semis) and I don't think there's much between the two. However, I've not seen the 2011 final in a long time and I've only ever seen a few points from the 2004 SF so the jury's out here.
Miami: Yeah, this is obviously Nadal. Though this was historically Agassi's most successful tournament, he lost to a guy I've never even heard of in an early round while Nadal put up a very good fight against Djokovic in the final that ranks among the pair's best Bo3 matches.
Canada: Both guys had disappointing tournaments here but Agassi advanced one round further while Nadal lost in the opening round to Ivan Dodig (weird scoreline too). Agassi was better here, but there's not much in it.
Cincinnati: Clearly Agassi. Nadal got straight-setted by Mardy Fish in the QF while Agassi won the whole thing beating a fairly respectable draw including Fish, Johansson, Moya, Roddick, and Hewitt.
US Open: I do wonder if Agassi would have reached the US Open final had he been placed in the opposite half of the draw. After all, Hewitt stunk up the court a bit in the final while Agassi played a great match against Fed (awful fourth and fifth set conditions notwithstanding). I genuinely think that's what would have happened and the fact that the Federer match was a QF rather than a F unfairly taints it in this comparison. Meanwhile, Nadal had a nice road to the final including a win over Murray. I wasn't impressed at all with his match against Djokovic though. Outside of the third set, Nadal was well below his 2010 level. His serving, for example, was perhaps the poorest I've ever seen from him in a Slam final. Now, that third set redeems the performance somewhat (even if his languid fourth set tried its hardest to undo all of that), but I still didn't walk away terribly impressed. Agassi takes this imo. However, Federer from the 2011 SF beats Agassi.
The fall Masters are tricky to compare between these two eras because Shanghai and Madrid Indoors don't line up all that well, so I'll just list what they did at each event without comparing them:
Agassi:
Madrid: Made it to the SF and lost to Safin in straight sets.
Paris: Skipped
ATP Finals: Did Not Qualify
Nadal:
Shanghai: Made it to R3 and lost to Florian Mayer in straight sets
Paris: Skipped
ATP Finals: Qualified, lost to Federer and Tsonga in the RR, prematurely ending his campaign
I think 2004 Agassi's hard court results were better than 2011 Nadal's due to his advantage at the AO and US Open. Where 2011 Nadal picks up the slack are his performances on clay and grass where he played quite well overall while 2004 Agassi straight-up sucked there (he didn't even win any matches on either surface).