Dealing with different voltage needs on a battery driven low-power board
Because your system spends the majority of it's time in sleep, I would go with the first option as it is the simplest and eliminates problems with differing battery lifetimes.

I would use an ultra-low Iq linear regulator (numerous solutions exist for this) to derive 3.3V and feed this directly to the MCU.

I would use a power switch (just a P-channel MOSFET) to power the sensor from 3.3V as required.

I would also use a P-channel MOSFET to gate radio power direct from the battery.

So the MCU can wake up, turn on the sensor, take the reading(s), turn the sensor off, do any necessary processing, turn on the radio and send data, turn off radio, go back to sleep.

The total current draw in sleep is MCU + regulator Iq. I did not consider a switcher for 3.3V as it is difficult to get low regulator current in operational mode (which the MCU needs). That said, I had this device featured in my inbox this morning.

There are other ways, but this seems the simplest.

Note that there is interface logic capable of interfacing across circuitry when one side is powered down but the current draw in this mode may be too high in this application, but there are other ways of ensuring no current paths exist from a live area of a circuit to the powered down zones.