The Flushing Meadows mini golf course is a true diamond in the rough. My wife and I discovered this as we were trying to figure out birthday party plans for my son. We went in the beginning of June and took our time going over the course. We finished in about an hour and a half (2 adults, 2 kids), and had a blast. We returned at the end of June, staked out some picnic tables and setup a birthday party serving about a dozen children, halfway through the course we stopped keeping score, but the kids loved the challenge and the environment. Keep in mind that this is a Parks Department facility, so you won't see Spongebob-pineapple-houses anywhere, just simple putting greens. No frills or amusement-park style attractions. It's a very spartan, basic course, but it's still challenging enough to be fun. The staff are very helpful and informed and the facilities got a makeover just this year (around May 2012). The snack bar is fairly extensive and the bathrooms are immaculate!
All in all this is a place we will return to regularly. The best part is: no one knows about it! There's never any lines, or crowds of rowdy, screaming children running amok. It's serene and relaxing.