The only reason you would want to remove water heater nipples is if they are leaking or so badly corroded that they look like they will start to leak. They really aren’t something you would choose to do normal maintenance on. However, be careful how much you chew off here…sometimes it is as if the water heater nipples are welded into the tank.
After you remove the supply lines at the top of the nipples, try some penetrating oil around the threads (where they enter the tank) and wait. The oil may or may not help, but the answer lies in leverage. Use the biggest pipe wrench you can find and place the jaws around the unthreaded surface at the midpoint of the nipple. Then try to unscrew the nipple. Then try some more. With any luck, you will hear a “snap” sound, and the nipple will start to unscrew. You don’t want to hear that sound and have the nipple shear off. It’s a gamble, but there really isn’t a foolproof method to removing these. If the nipple does shear off, your day just got longer. Here is some information on how to remove a sheared off water heater nipple.
Use dielectric nipples to replace the old nipples. They won’t corrode like the old ones did.