Boot strapping Vs Charge pump
A charge pump will give you more flexibility. 

Bootstrapping is essentially a charge pump operated by the main switching devices.

The advantage of bootstrapping is low cost - usually a single external capacitor and a diode. The diodes is internal to the driving IC if an integrated driver IC is used.

A separate charge pump requires a clock and typically two diodes plus s pump capacitor. The components (usually with caps external) my be contained in a custom charge pump IC. This takes more room and may cost slightly more than bootstrapping.

A charge pump has the following advantages.:


Still works when duty cycle approaches 0% or 100% (unlike bootstrapping).
Works with load switching as slow as you want.
Not forced to comply with constraints imposed by the main system - eg clock speed. 


In your case the last point is probably major. You can design the charge pump to work optimally without having to deal with a high clock rate or load driving behaviour. 
However, many people use bootstrapping with acceptable results.