You can get money in 2 ways;
~Sell anything that you don't need or use; if you think you might use something in the future (evolution stones), then keep them.
~Do tons and tons of battles with Lv.38-Lv.45 pokemon. I have been leveling up my pokemon at the very top. After about 15 or so levels, I had something like 75,000. Then, I sold a bunch of stuff and leveled up some more pokemon. It took awhile before I got enough (depends on what you're fighting), but you can eventually build up a lot. I ended up buying 99 hyper potions, which came out to be 118,800.