Was it a Vong ship? He says it was unlike anything he'd ever seen, with highly advanced weapons, and it left the known galaxy. All of that points to the Vong. Sorry if I'm slow at picking up on this, but it's been a long, LONG time since I went through that conversation with him, and back then I knew nothing about the Yuuzahn Vong.
it was not a "ship" it was a non-sentient creature created by the vong to act as a probe.