If you are using 9 ounces of water for 16 ounces of flour, your hydration percentage is a little over 56%, which is at the low end of the range for a New York style dough. If you are using "over" 9 ounces of water, as you indicate, then you would be moving further into the hydration range depending on how much over the 9 ounces.
As for the other ingredients, it seems to me that 2 t. of instant dry yeast (bread machine yeast) is too high relative to the amount of flour used. If you are using 2 t., I would suggest cutting it back to about 1 t. Too much yeast can cause a dough to overferment, even in the refrigerator, and cause carbon dioxide to escape and result in a weakened dough structure with poor oven spring. I would also try cutting back the salt to 1 t. Salt regulates the fermentation process and cutting it back should allow the dough to increase its volume (and compensate in part for the reduced amount of yeast) as opposed to tightening the dough and inhibiting its rise. The rest of the ingredients seem to be within the normal ranges for a New York style dough based on what I have seen from the recipes and the favorable results posted at this site.
Often, a simple step that can be taken to increase dough volume and increase the number of holes in the crumb is to increase the amount of water used. This is basically what is done for breads like ciabattas, which are full of large holes. The increased water content should also improve the crispiness of the crust. Another step that you might take is to let the dough rise for a half hour to an hour after you have formed and shaped the dough into a dough round and before dressing and baking. Usually, when a refrigerated high-gluten dough with added sugar is taken out of the refrigerator, it can tolerate several hours at room temperature before forming and shaping. So you have a fair amount of time to let the dough rise before shaping, etc.
Other small steps that might be considered is to add a little bit of milk (scalded and then cooled) for part of the water used in the recipe, to provide added softness to the dough. Also, substituting honey for the sugar (and slightly reducing the amount of water to compensate for the liquid in the honey) may also help provide a softened crumb by coating the gluten strands more effectively than sugar. The combination of olive oil and honey serve to trap the moisture in the dough (as well as flavors) and also to slow down the gelatinization of the starch and the coagulation of the gluten during baking, resulting in a softer, more moist crumb. I must warn you however that using these approaches may produce a more bread-like character and not have the more characteristic "New York style" chewy and leathery quality to the crust.
I think the biggest factors to accomplish what you are looking for is to increase the amount of water used, and let the pizza dough round rise some before baking. If you are using a pizza screen, you can also prebake the dough round (you may have to dock it first) before adding the toppings and finishing the baking. This should allow the dough to have a better oven spring, unimpeded by the weight of the toppings. You didn't indicate what bake temperature you are using, but you might consider lowering the temperature a bit to allow the pizza to cook a little bit slower and longer.
While it isn't usually recommended, if you want a lot of bubbles, you might consider working your dough while it is still cool coming out of the refrigerator, i.e., shaping, dressing and baking it. The cutoff temperature is around 50 degrees F, that is, you will get the bubbles if you bake the dough when its temperature is below 50 degrees F (and sometimes above that if you are using a lot of yeast). You may have to dock the dough and you may get larger bubbles than you want, so you may have to experiment with this approach to get it where you want it to be.
The thing that puzzles me most about what you have reported is the stickiness of the dough you have been getting from your recipe. You may want to carefully weigh the flour and water as a start, and make adjustments to flour and/or water to get the dough to the point where it is sufficiently kneaded, soft and elastic and capable of passing the windowpane test.