They are roll pins. They are not threaded. If you don't have a punch you can grind the point off a nail and use it to drive them out. Actually you only need to remove the bottom pin and the gear will slide off.

Where did you find the replacement nylon gear? Thanks.

stylin63 you can get the nylon gear at Sears or most any door opener service company. The part number is 41A2817.

I wanted to add my 2 cents, even though this is an old thread, because folks searching these boards still find it. I could not get those pins out either! But turns out for just a few dollars more you can get that gear already mounted on the shaft with a new bearings, chain sprocket, the works. And it beats pounding those pins out overhead! I put the instructions on a web page:
http://dl.dropbox.com/u/1347192/lifter/liftmaster_repair.html

Here is a link that might be useful: sears craftsman garage door opener gear repair / replacement instructions