Are you staying Club Level? If you are, the CL concierge may be able to help you get reservations for a time you want. We asked and were able to get a prime time for California Grill within a month of our reservation.
I recommend the Club Level to you for a number of reasons, and for similar reasons want to caution you about Ohana's. We would love to convince friends of ours to come to Disney with us - their son has Aspergers and OCD, and have thought that the Poly CL would meet their son's needs, so wanted to answer your post.
Ohanas: If your child can become overstimulated with noise, Ohana's tends to be on the loud side, and my only experience has been from walking by the restaurant, and experiencing it as very loud from outside the room. If your son would prefer something less stimulating, I would instead recommend Kona Cafe. It is lovely, the food is excellent, and it is quieter. It is now probably our favorite restaurant on Disney Property (except perhaps the California Grill.) There was also not much wait at all when we dined there (4 minutes as most, and neither time did we have a prior reservation, though I would recommend one.) The chairs outside Ohana's were filled with people waiting for their tables.
I recommend the club level because the lounge will become familiar to your son, it is MUCH quieter than the resort counter service where I would assume you would have breakfast every day - breakfast is served every day in the lounge (oatmeal, cold cereals, fruit, coffee, juice, sometimes cinnamon rolls, sometimes croissants) and the lounge is much quieter and calmer than Captain Cooks during breakfast time. While we did very much like being able to order late night flat breads for our teens, my dh and I walked through Captain Cooks one morning, after an early morning relaxing stroll around the resort, walked into a wall of noise. I turned to him after leaving and stated how grateful I was for the CL lounge. He laughed and said he had just been thinking the same thing. Captain Cooks was packed, children were crying, it was just tension inducing just walking through it. Maybe it was an off morning.
You can also watch the fireworks from inside the CL lounge, which may be less overwhelming than in the park. The lounge also has two televisions, one upstairs and one downstairs. The CL includes milk, soda, beer, wine, coffee, water, breakfast, afternoon snacks, appetizers and dessert. For us with the 40% off it cost only an additional $84 a night. Very much worth it. We paid OOP for four sit down meals and perhaps three counter service meals, and a few snacks, but the breakfast/appetizers/desserts/snacks and liquids were more than enough food otherwise.
If you will be spending more time at the resort than usual, it may be nice to have the appetizers at dinnertime at times, and if you wish, you could take meals back from Captain Cooks and eat them in the quieter lounge, though I would recommend a table outside Captain Cooks. It is very pleasant.
The transportation will be excellent for you from the Poly. Just as a "heads up" if you ever decide to take the boat back to the resort (lots of fun) that your two year old will not be able to sit in the stroller - if I remember correctly, strollers need to be folded on the boat (please correct me, everyone, if I am wrong!) You could, however, walk over to the TTC and use the stroller on the large ferry. The monorail would probably be easiest, though we really enjoyed the boats.
I know that you will enjoy the Poly. Just wanted to say that my friend's son would find that it would meet many of his needs - a quieter, familiar place with dependable food, and an area to call home (besides the room.)