I agree with the others. Going wih a significantly shorter bulk time will help get rid of most of the large bubbles. I think what happens during a extended bulk fermentation is that the gluten strands are strengthened. So when you ball the dough fairly late, it's common for those stronger gluten strands to trap air (bubbles). These air pockets that are initially formed during the late balling can also get bigger as John mention during the later stages of fermentation when the gluten matrix starts to break down. The thin walls around the air pockets can break down causing multiple air pockets to coalesce.
The 2nd way air can get trapped into dough is during the balling phase itself. Depending on the technique you use to ball the dough, you can cause more or less air to be trapped. I think for a NY style a lot of people like to see those larger air bubbles as oppose to the NP style where people don't seem to desire them.
However, going with a shorter bulk fermenation time will also yield noticeable differences in the final crumb textures. So you will have to do some experimentation to see what you like best. If it were me and I was happy with the current crumb texture, then I would keep it the same and just use a skewer and pop the big air bubbles before loading the pie.
