If you go back and read, Naruto also got a couple other hits in, and before the final hit when they both meet and hit it specifies that the attack was devastating to both (why they were both put into craters) but Naruto probably had the worst of it due to Kaiten helping Neji. But Naruto is nothing if not a stamina freak.

Also, Neji wasn't expecting the hit from Naruto, and as was said it was a Kyubi Naruto punch. Look what that did to Haku? Granted that was more Kiyubi, but even still, definately not what I'd call a weak punch.

Against Spider-Guy, Neji's chakra isn't as depleted, and all of the hits he's been expecting and so has at least braced for them. It's not much, but it would help out somewhat.

Oh, theres also the fact that here, technically speaking, Neji is fighting for those dear to him, as he's taking Spidey on so the mission can be completed by his friends. And we already know what fighting for someone will do for you in Naruto (i.e. Naruto vs. Gaara, Sasuke vs. Orochimaru, Naruto vs. Haku, etc, etc)