Hmm...I like both bands and have seen both twice.
TOOL is great because of the excellent musicians in the band, while APC is great because of their songs. I don't think I could say one is better than the other unless it's comparing MJK's role in the band...his vocal talents are more utilized in APC, but I couldn't imagine TOOL being what it is without his voice either.
Do you have the DVD with the various videos on it? The "Bikini Bandit" stuff was just too strange. I received it as an Xmas present, but I probably wouldn't have bought it on my own.