From Daizenshuu 2:
Defeat Boo!
Goku fought with the revived Boo. Goku tried to have the next generation resolve this problem, but in the end he was the one who defeated Boo, the strongest in the universe, after being resurrected by receiving the life of the Dai-Kaioshin. Thereupon, he meets with Boo's reincarnation, Oob. In order to raise Oob, who didn't know how to fight, he flew off.
So it’s flat out stated that the Boo that Goku defeated at the time of his defeat was the strongest in the universe. Gohan was there for Boo’s defeat; he even contributed to it. And as you'll recall, his contribution, which should have been all the power he could muster, was totally insufficient.
You’ll also recall that (based off of translation from the original Japanese manga) Goku initially thought that Vegeta planned on having Gohan AND Gotenks AND others come and help fight Boo.
Now… what would be the point of having Gotenks come if Gohan could handle it alone easily, or vice-versa?
For that matter, how desperate would they have to be to bring the fodder along too??
That just shows that the Pure Boo is nothing to snort over.
And what about Vegeta’s speech? He flat out said that Goku is the only one who can fight Boo (he himself is dead and fighting against Boo, if not at the moment, so there’s no reason that other dead people would not be able to fight Boo too.), not that Gohan can do it too. He also calls Goku number 1. If he’s not actually the number 1, what the hell is that whole speech about exactly? It’s basically just a “Goku kicks ass + Vegeta character development” speech.
Vegeta’s also not the type to arbitrarily say somebody is strongest when he knows damn well they aren’t. He acknowledges people’s powers and their placements.
Anyway, back to Daizenshuu 2, it’s stated in the Final Battles section that “even a Full Power Goku can’t defeat him [The Pure Majin Boo]”. So Goku is clearly not strong enough to defeat Boo himself.
It’s also made clear in the manga that Boo was playing with Goku, not taking him seriously; so any claims that Goku was fighting Boo “evenly” are somewhat misinformed.
It also states that when Goku is about to finish Boo (when he wishes to fight him again) that:
Goku's feelings are only understood by his fellow strongest.
So there it’s established that Goku and Pure Boo at that time are the 2 strongest, and it’s otherwise established that Boo is stronger than Goku.
Nonetheless, Goku being second strongest still establishes him as stronger than Gohan or Gotenks.
Another instance where this is pointed out is after Boo is beaten and Vegeta is about to kill the Good Boo.
Vegeta asks who will stop Boo if he goes mad again; implying that he’s stronger than anybody, and clearly to strong for Gohan to stop if that question has to be asked.
Then when Goku answers, he says that he’ll be training so that he won’t lose; implying that he was weaker than Boo was at the time.
Even 10 years later though, where Goku is stronger than Gohan, he still thinks there’s a chance that he could lose to Uub’s Full hidden power, which should be that of Majin Boo.
Now, to counter the common arguments, logically, how much stronger could Shin Boo possibly be? Given that it’s established that SSJ Gohan was stronger than any of the Kaioshin (by virtue of being able to pull out the Z-Sword), even Buff Boo, who is significantly stronger than Shin Boo, couldn’t even have a gap between him and the original Boo as great Gohan’s SSJ power.
That’s even assuming that South Kaioshin made Boo stronger, which is never stated to be the case. Given the lack of a plural form in Japanese, it could be that absorbing any of the Kaioshin made Boo weaker.
Either way, considering that Fat Boo is weaker than the Original Boo, the combination of Dai Kaioshin and South Kaioshin was detrimental to Boo’s power. Therefore it makes sense that removing both of them (which is what removing the Good Boo from Shin Boo’s body did) would make Boo stronger.
In that very scene, Kaioshin states that the heart that was making him weaker (when the form he was just in was Shin Boo) had returned to normal. That seems pretty clearly to be a statement that Boo just got stronger than what he just was.
Speaking of removing Boo from Boo…
There are plenty of explanations why Goku seemed to show fear for Shin Boo.
1) Goku’s personality had been completely off the entire Boo saga, he even tried to get others to fight his own battles for him. I’ve done a more detailed analysis on this before, if you’re interested.
2) Goku’s sensing was thrown off by being tiny.
3) Goku didn’t want to upset Vegeta. This explanation holds more credence than you might think. Vegeta had already expressed his loathing for Goku’s ascension, and Goku had previously gone as far as risk death in a fight with Vegeta to avoid showing it to him or letting him know about it. Goku would never show Vegeta the form unless Vegeta approved of it first (and only used it in front of him AFTER Vegeta had specifically asked to see it). This is also shown by how Goku only transformed into a SSJ when confronted by Shin Boo, rather than a SSJ3, which he easily could have done.
The fact of the matter is that Goku should always want to fight with strong opponents, both by 10 years of that being his character, and by Akira Toriyama’s statement on his character and greatest wish. And even if Goku wasn’t particularly keen on losing at that point, he still never displayed cowardice and fear like that.
There were too many things off for there NOT to have been a difference. And who knows; Goku’s change in personality may have affected his power by means of Shouki and Yuuki? This is actually a very important point, as it's quite clear that for the majority of the Boo arc Goku is not acting like his normal self. He's passing on fights even when he could win them, he's acting oddly out of character. This could easily justify a loss of shouki (right mind/true character) and as such a loss of power. Yuuki (courage) is also an aspect of his power that could have been greatly diminished by his fear of fighting Shin Boo. Now, by the time that Pure Boo emerges Goku is back to his normal self, he just wants to fight a strong opponent and have a good time doing it. Back to his regular state of mind, it's possible Goku's shouki and yuuki returned to their full extent, pushing his power beyond that of Gohan.
I’ll just end this on a statement made in an interview with Akira Toriyama himself in Daizenshuu 2, after the series was over.
Q: Out of all your characters, which one is the most cool?
A: I think it's Goku. The always pure strongest in the universe. Goku is #1 after all!
And there you have it. Goku is the strongest. And if he's stronger than Gohan and can fight almost equally with Pure Boo, then Pure Boo must by extension be stronger than Shin Boo.
