There are a few statements which suggest that even base Super Boo is superior to SSj3 Goku, who is a peer to Pure Boo. Such as:
Chapter: 498 (DBZ 304), P2.3-4
Boo: “Far, far, waa~~aay far away, I felt a strong power…I won’t allow anyone to have a power stronger than mine…”
Super Boo has Fat Boo's memories and remembers his fight with SSj3 Goku, yet only shows concern about being surpassed once he senses Gohan's power. Not to mention this statement:
Chapter: 507 (DBZ 313), P12.4-5
Context: after Goku and Vegeta revert Boo back to regular evil Boo
Goku: “Hehhe~~eh! With this, Boo’s power should have fallen significantly! We’re almost there! See, see: the size of his ki is completely different than before!”
Vegeta: “Alright! Let’s blast out of here and escape!”
Goku: “Wait! Even though Boo has returned to normal a whole lot, we’re still simply no match for his strength! If we go outside like this, we’ll definitely be done in…!”
And even if you want to argue that Goku didn't want to hurt Vegeta's pride by using SSj3, Boo himself shows complete confidence in taking on both Vegeta and Goku even while knowing about Goku's SSj3:
Chapter: 507 (DBZ 313), P4.2-4, P6.3-6
Context: as Goku and Vegeta are attacked by evil Boo
Goku: “Alrii—iight! Come at me if you’re gonna. I’ll open up a huge hole inside your body! *Boo smiles* Wh-what are you smiling about?...Do you think I can’t open one?”
Boo: “It’s no use.”
Goku: “Don’t underestimate me.”
*Goku blasts, not much happens*
Goku: “…”
Vegeta: “…It di-didn’t have any effect…”
Boo: “It stung a little here *points at head*, that’s all. You guys are now far, far smaller than fleas.”
Goku: “…So we’ve got no choice but to defeat you and then search for an exit somewhere.”
Boo: “No, you can’t defeat me. Not the way you guys are now…You’re gonna die, not me…”
Now I suppose you could argue that Pure Boo was holding back against Goku and his true power is greater than Super Boo's, but Goku being able to wipe out Pure Boo with a minute of charge time is never outright contradicted, and thus it's debatable whether or not a full power Pure Boo would really be able to fight against Super Boo. At the very least, Super Boo > SSj3 Goku should be pretty set in stone, and thus the answer to the question in this thread comes down to whether or not you consider SSj3 Goku to actually be on par with Pure Boo or not.