IMHO, just replace the axle. A brand new axle with new boots already installed is about $90 from NAPA. It will save you a whole lot of time/mess/hassle.

As for your current axle, if you plan on keeping it and replacing the boots, then do it ASAP before the lack of grease causes damage. If you don't plan on keeping it, it will likely work ok for quite some time before it starts clicking unless you use 4wd a lot.

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik