SSJ3 Gotenks is stronger. He was clearly superior to Super Buu when he fought seriously, was mentioned to be barely weaker than Mystic Gohan. Not to mention, in a living body back in Z at least, SSJ3 drained Goku considerably, but on the other hand, the fusion doesn't last long, especially when Gotenks' turn SSJ3 where it also drains the fusion timelimit considerably
The only advantage SSJ3 Goku would have is fighting experience over Gotenks' childlish behaviour, leaving him open to attacks and considering that at full power, Goku was mentioned to be stronger than Fat Buu(which is a reverse of Super Buu, but with Super Buu able to use more of his latent power due to evil side being stronger) and Kid Buu, a single mistake could be detrimental
So if Gotenks fool around like he did at the beginning of his battle with Super Buu, Goku could have a shot with a instant transmission + full power kamehameha combo.
Otherwise, SSJ3 Gotenks would overwhelm him