For new pipes I run a bristle cleaner thru the stem a few times and see if big stuff comes out (both in the stem, and the pipe itself. You never know what might be hiding in there from the factory. Then I dip a pipe cleaner in Everclear or Whiskey and repeat til it comes out clean (most times one is plenty).
After that, if the stem is in fairly decent shape I just grab a small piece of recycled t-shirt and hit the stem with a good gritty toothpaste and rub away. Rinse and repeat a couple times if that pipe has been "on the shelf" long enough for it to discolor. If it's a new pipe and the stem isn't oxidized, I only do it once to get rid of the "sticker goo".
I give it a final rinse, rub it dry, and start plotting what I'm gonna break that new pipe in with!
Welcome aboard! First off, if the pipe is new, just blow through it to make sure it's clear, then dip a pipe cleaner in high proof alcohol and run it down to the bowl. After that, you're good to go!