MLCC Shortages and Work-Arounds
If you can respin your board, there are few things you can do:


As stated in the comments, use larger package. 0.1uF/100V might be easier to find in 1206 than 0603.
Use 2 (or more) lower value capacitors instead of one higher value capacitor. Advantage: lower ESR/ESL, Disadvantage: Lower ESR/ESL, depends on your design.
If allowed and properly evaluated, use different dielectric. Y5V might be easier to source than X7R. 
If you need the higher voltage, use 2 capacitors in series.You will need balancing resistors, which will consume power.
If cost is not an issue, use Tantalum or other exotic types. Again, this opens up some major reliability concerns, so tread carefully.