Even the pyramids are not guaranteed to survive that long.
You could engrave something on the really hard crystal and make sure the words and the crystal are big enough to keep the shape under conditions. The degradation of the shape could be calculated by a chemist. Then put it in to a mountain cave, you need to talk to a geologist here and find the area with the caves that are really old, there are plenty, some mountains are more or less stable for millions of years.
But then again, how you let the receiver know where to look for your message. And do you care who exactly is going to find and read it? And why should they care? They would care if they knew this some how helps them in their lives. So it must be about them. Like we are really curious where our civilization came from, that's why we keep looking for old messages. So basically to make them interested in your message, you need to some how change their lives. And leave a track to a message.
But assuming you can change their lives, which means to have some influence on the society, it is easier to leave the message in the society to pass on in the form of useful idea. That's maybe why religions were created and continents conquered, the greats of the past wanted to leave us the message.
Since we do not know how to create mental entities that would survive in the society for so long, maybe you can choose to modify human genome, and then the scientists of the future will decode your message.
But in fact, I believe that once you left your message here on Stack Exchange, it will most certainly survive for 50000 years. Because this site was created to accumulate knowledge, and is one of the first more or less successful implementations in this area, this site and the dump of all it's database is almost certainly guaranteed to be backed up and copied into all future implementations of knowledge gathering. Once they create quantum computers or even pure-energy computers or any other advances in information processing and storage will be made - most important data will be copied over from old systems. Like those floppy discs, billions of floppy discs are dead, but most of even slightly valuable data from floppies is now stored on hard discs or SSDs, in the cloud or you PC/tablet/phone. And surely future data storage devices will allow super cheap copies of whole Stack Exchange network.
So leave your message here in the comments and add a hashtag #tobereadin52014. So the "Bing" of the future will be able to find it and let the whole mankind "retweet" instantly around the galaxy or whatever. And don't worry about the language, translation tools of the 52014 will easily decrypt your ancient scriptures online. You can even add some formatting and hyperlinks. But probably only few hyperlinks will still work in a distant future. At least those that link to another stack exchange page are surely safe.
