I feel like it might be incorrect to consider characters in Usagi's world(s) that originated in TMNT media to be Crossover Characters. Characters like Sumo Kuma, I'm almost positive have never appeared before Yojimbo in any capacity. I also think calling them Usagi characters might be technically incorrect, but I'm willing to be a bit more lax on that.
It's also hard for me to consider characters like Kakera, who have only ever appeared in TMNT/Usagi crossovers, as well as some C.O.W.Boys characters that have done the same.
This is one of those things where I will defer to you folks.
Yeah I try to keep up with Usagi but it's been running for so long and there was a long period where I didn't buy comics, so I wasn't sure I had missed something. But I had done a cursory search myself, and seen nothing outside of this show mentioned.