MOSFET Driver increase maximum duty cycle
Before increasing the size of the caps I would check their capacitance at the voltage you are using them. In several cases, the change in the capacitance values with the bias DC voltage can be massive! Check this page to get a better idea of the phenomena.

Now if that is not the issue, I think that increasing the size of the capacitor will be the most reasonable option. If you are afraid of burning the bootstrap diode, you can include a small resistor in series with the cap. I have seen some designs with this modifications and they work fine.