Most of the replies here are outrageously wrong. Boo Saga SSjin 3 Goku doesn't stand a chance against Base Gotenks (post-training).
SSjin Gotenks (pre-training) was stated to be stronger than SSjin 3 Goku, and no one denied it after Gotenks was formed. Piccolo thought SSjin Gotenks would get decently stronger in the RoSaT, but turns out to be totally wrong. He was a lot stronger. He didn't expect SSjin Gotenks (expected, post-training) could beat Super Boo, but after witnessing Base Gotenks (post-training) formed, he said he could have a chance.
Base Gotenks (post-training) > SSjin Gotenks (expected) > SSjin Gotenks (pre-training) > SSjin 3 Goku.
No need for SSjin 3 Gotenks at all. However, if EoZ Goku is being used here, it will end up differently.
EoZ Base Goku was implied to be close to his Boo Saga SSjin 3 incarnation, at the very most as strong as it or a little above it. Let us say he's nearly as strong. The chain would end up as this.
Base Gotenks (post-training) > SSjin Gotenks (pre-training) > SSjin 3 Goku ~ EoZ Base Goku.
Still, Base Goku is weaker than Base Gotenks. So if both of them were in SSjin 3, the gap would be the same. Gotenks would most likely defeat him at that point, but there's a slight chance that Goku could take this.