So I've taken Super Shuttles about 5 times now. All from Manhattan to JFK. Two were during normal (daylight) hours, and three were at around 3:30 AM.
On my first ride, I found out that each blue van is its own franchise, and they're just routed by the parent company. This leads to some fairly ridiculous situations, as there are adversarial relationships set up between the client and the driver, the client and the parent company, and the driver and the parent company.
A typical scenario is to go outside to wait for the van, wait for half an hour, and then nobody shows up. Both times I tried to use the service during the daylight, they didn't show. I called, and they blamed it on the drivers. I was not issued a refund.
Another scenario is to be riding around in the van for four hours (they pick you up three hours before your flight) as the driver wanders aimlessly through the city looking for more passengers. You call Super Shuttle on the phone because you just missed your flight, and they blame it on the driver. The driver, in turn, blames it on the guy routing him. They don't tell you that the whole point is to have two scapegoats to misdirect you while you try in vain to complain.
Both parties are only interested in as many people as possible being taken to the airport, and customer service is avoided by this planned misdirection. It's quite clever, actually.
I've actually had fine experiences on my middle of the night runs, and wasn't picked up at all on either of my daylight attempts. Why do I keep using them? Well, I've had good luck in the middle of the night, and I'm poor. A cab ride costs about $40, and they cost about $20.
Just now I had my best experience ever. Only six passengers in the van, the driver thanked me for going down early, and I got to the airport within half an hour. I'd rather sit here with a wireless internet connection than sit in the van with annoying passengers.