I have a very strong preference for air brakes, but I will admit I am biased, and have a great deal of experience driving large air-brake equipped vehicles. Also, since my driveway is not flat, I wanted (needed) maximum possible holding power for the parking brakes; more than any driveshaft mounted brake could provide (and if I raise one wheel to change a tire or service the brakes, it renders the driveshaft brake useless).
That said, many thousands of hydraulic brake buses are in service with no issues and can be said to be just as safe as their air brake equipped counterparts (assuming proper maintenance, in both cases).
Ultimately this comes down to the same thing as "which is better, Ford or Chevy?" Both are good and they are fairly close to the same, they do the same job. So which is your preference? My suggestion - see if you can test drive one of each, and which you prefer.
One last *VERY IMPORTANT* thing - air brakes do *NOT* have the same pedal travel that hydraulic brakes do! Hydraulic brakes may have a few inches of pedal travel. For air brakes, this might be more accurately measured in millimeters! Air brake valves are, for all intents and purposes, a foot-controlled pressure regulator. The more pressure you give it, the more pressure it sends to the brake chambers. The valve is self-equalizing the whole time, so the pedal never really travels much beyond the equilibrium point. None of this is a bad thing, it's just different and something you should be aware of when driving one for the first time.