Well, technically speaking, a "nanite" IS a "nanoprobe," as the terms would be, in real life, interchangeable, as both merely refer to any type of microscopic robot performing tasks at that scale. They don't even have to be able to do it autonomously to qualify, though for practicality reasons it certainly helps.
What it'd really boil down to is how they are built and/or programmed at the end of the day, and theoretically, both could be made to do the same functions as the other fairly easily and mostly only through some changing of their core programming, not structural design, even further narrowing the differences between them.
But considering the functions the two are traditionally shown to exhibit in Trek, then I'd say, for the purposes of the poll, the nanites, if only because they clearly possessed a much higher level of intelligence overall (though that may be because they operated as a group and thus shared the workload between them...TNG wasn't super clear on that), at least in the particular episode referenced (that was, after all, a rather unique case for the tech).
