I would highly recommend going to the Contemporary and trying the Contempo Cafe.
As for what to eat here are my favorite items on their menu. Chicken Caesar Salad with the dressing tossed in, Pepperoni Flatbread Pizza and their Spice Crusted Mahi Sandwich.
Love Capt Cooks at the Poly....excellent chicken or veggie lo mein and the BBQ pork sandwich or adult grilled cheese with housemade chips are both great choices.
I can only speak to Captain Cooks at the Polynesian. First, it is very close to the monorail station. Second, they have food my daughter will eat (e.g. Flat Bread -- near equivalent to personal pizza). For lunch I really like stir-fry noodles.
Just wanted to say the Contempo Cafe is also close to the Contemporary Monorail station and it's actually closer since both are located on the 4th floor of the Contemporary Tower.
At the Polynesian Captain Cook's is located on the 1st floor of the GCH and their Monorail station is located on the 2nd floor.
Going to stalk this thread, if no one objects. Didn't even think about trying to eat at another resort (aside from the Poly for Best Friends Breakfast).
Contempo is one of my favorite CS locations in WDW. It has good mainstream favorites as well as several unique items and the cupcakes are AMAZING. My other favorite monorail spots are Kona and the Grand Floridian Cafe. Both are fairly efficient for TS and have reasonably priced items. I know you asked about CS, but I figured I'd mention them since I opt for them sometimes instead of CS because they don't take up a lot of time.
I would vote Contempo Cafe. We stayed at BLT and ate there at least once a day every day of our visit. It really was good. My favorites were the Honey Lime Chicken, and the Caesar salad. My DH really like the Marinated Steak Flatbread. http://allears.net/menu/menu_contempo.htm