Step-down voltage directly or in intermediate steps?
This is really two questions I think, a dedicated 5V rail question, and a large DCDC step, so I'll try and answer them each.

Dedicated 5V rail
There are advantages to having a dedicated rail for some devices some times. But they are high noise, or high sensitivity areas. Keep it all at 3V3 and you'll find it easier. The only other time to have a dedicated power supply is to simplify layout/routing, but your system doesn't sound like it's complicated enough for that to be a concern.

Big step of 60 to 3V3
I would say this is less of an issue than you think. While it could be noisy, having only one switcher means you can control the output and the input to it should be simple. Putting two switchers back to back can get complicated with noise, as they each could effect each other which could make noise better or worse depending on so many factors. No idea if cost is important, but it is almost always cheaper to have one switcher to do it all, as this also means less passives etc.

Another way to look at it is losses: two switchers will each have their own losses, it may not be double the losses, but will be more than just having one supply. If you have a power draw of 100mW, with two switchers, each at 90% efficient, you're getting 81mW at the components. Meanwhile if you only had one switcher, you'd be getting 90mW.

A single step change would be best.