Yeah, I'd go with what grinder says. Try and tackle the problem before recording.
I've tried different strings (Elixirs are good), different mic placements, and (*gasp*) even concentrating on my technique while playing. You can minimize squeaking while playing if you really concentrate on it. That way you do as little modifying to the recorded track as possible.
Obviously, this is no help if that track is THE definitive track and you want to save it ;-)