Was getting ready to repaint the bottom on my Borealis XL when I noticed the two blisters in the pics below.

What's the best way to repair this?

It's so nice to do repairs on an area that's going to be repainted! :-)
My approach:
I'd remove any 'loose' glass and then feather the edge of the glass and a good area past the edge of the problem (removing the paint). Don't be timid - you are going to be repairing it and it's not much more trouble to do a large area than a small one, so don't leave any areas with 'half-bonded' glass.
I'd also give the exposed wood a good scrub with water (in case it was amine blush that caused the bonding problem) and then sand it with 80 grit.
Re-glass the larger area, and top it with epoxy and filler as the 'fill coat'. The smaller area could probably be just filled with thickened epoxy mixed with milled glass fibers. Or use a small piece of glass there also.

Putting a piece of (non-wrinkled) plastic over the (wet) repair can help to keep things 'flat' and reduce the amount of filling and sanding required.

Also, adding black tint (System3 black or other black additive) to the epoxy won't hurt if the paint is black. I use colored filler on the fill coat if I'm painting the boat.