A NEW axle will be new. A REMANUFACTURED axle will only be as good as the person who rebuilt it. And, if you are lucky that guy may have actually replaced the bearings in the joint!
I'd get the boots. It's not THAT hard to replace the boots but the learning process can suck if you haven't done one before and dont have anyone that can help you. There are really only two things to keep in mind when replacing teh boots; Make sure you use the appropriate grease for the appropriate type of joint ( the inner joint is a different deisgn from the outer and requires a different type of grease, should be supplied just make sure you put the right grease in the right joint ), and make sure you dont damage the clip when reinstalling the outer joint.
A little trick to getting the outer joint on over the clip is to take a section of the old boot clamp, wrap it around the clip, secure it tightly with a zip tie to compress the clip and carefully whack the joint back on.
There are two ways of looking at it, buy a new axle and save yourself the time and effort of replacing the boots...
Or, save money by replacing the boots yourself but sacrafice some hair that might turn grey from frustration, getting Extremely greasy hands, arms, clothes, face, hair, everything else and alot of time.