First of all, there is nothing wrong with mixing alchohol with ammonia. It even comes pre-mixed in some window-washing solutions and this is what I generally look for when cleaning a pipe. Ammonia and Bleach, however, combine to form a poisonous gas. And there is nothing wrong with putting harsh chemicals onto or into something you're going to smoke out of. You RINSE it before use and you're fine. The boiling point of ammonia, alchohol, or bleach is actually close enough to room temperature that you don't even HAVE to rinse it... If you leave it out for long enough (longer than you'd probably like) it will completely dissapate.
You can use ammonia or alcohol to clean a resinated glass pipe, but be sure not to use both together. Another way is to soak the pipe in efferdent and rinse it. For best results, you might need to scrub off the tough spots with a pipe cleaner.
Wow don't ever use harsh chemicals in something that you are going to smoke out of