I have several good ones... a couple I bought with Joysticks replaced. I am surprised you can't find new ones though.
Have you ever considered just rebuilding them yourself? I have done it with lots of consoles and controllers, but not with a Nintendo 64 controller.
Now I have to go research this.
**edit**
Well that was interesting. I just looked in my repair tackle box and I have three of them in there already. I keep a LOT of spare parts for game consoles and controllers, I just didn't remember having these as I don't remember every opening a Nintendo 64 controller.
Of the three replacement sticks I have, one has wires to be soldered and two have a connector on them that matches my N64 controllers board plug. I opened a controller and could change a bad stick in probably 5 minutes or so. One thing I do not know is what the quality of the replacements are.
A quick look on eBay shows new sticks as well as button pad sets... sticks ranging from about $3 shipped to $10... there are some lower and some higher however. I would at least spend enough to get one with a plug and not have to solder anything.
But out of curiosity... why don't you buy some "well described" original Nintendo 64 controllers from eBay? You can find new ones from time to time, but they will be $100 plus. I guess it depends on how important New is to you.
Here is one I would love to have...
Original Nintendo Controller... NEW! (But Expensive)
Here are two original Gray also...
Original Gray Nintendo Controller... NEW!
Original Gray Nintendo Controller #2... NEW!
MrBlackCat