Spent 4 nights (and 5 days) in Puerto Vallarta in December, and thanks to some advice from Chowhound (and elsewhere), we had lots of good food.
This was our favorite meal of the trip. Started off with a pitcher of margaritas, which were nicely balanced. Queso Rebecca was actually a bit disappointing. The red pepper dip was good with tortillas, but the panela cheese was a bit plain. Mole Oaxaceña and Mole Poblano were delicious and I couldn't decide which I liked better. Delicious fresh tortillas for making small tacos. Carnitas w/ salsa verde consisted of tender pork with a non-spicy green salsa. Very good. However, the chile en nogada was by far my favorite dish of the night. Served cold, which is traditional. The blend of flavors in the filling was amazing, with a good balance of sweet and savory. Slightly spicy chile, with a smooth white sauce. I was tempted to order another plate for dessert. I am actually a little sad that we didn't. We made reservation to eat here, which seems like a good idea during high season.
Restaurante Dianita, in Zona Romantica
We had breakfast here on our last day, and it was actually our best breakfast. Great chilaquiles (we chose red sauce), and huevos divorciados (green sauce was good too). With coffee, orange juice and some little rolls, this meal cost the two of us under $10 US and was super filling.
Restaurant/Bar La Maquina, on Malecon just south of the Rio Cuale.
We came here for drinks and snacks at sunset. The grilled shrimp skewers here were likely the same as elsewhere, but we got them hot and fresh, while sitting at a table right at the front (i.e. on the beach). Good ceviche, fresh chips, and some spicy green/avocado salsa. Nice with cold beers. Super casual and cheap, and ceviche portion was surprisingly large.
Ocean Grill, Boca
Like others have written, Ocean Grill was great. We did a day hike and spent several hours on the beaches near Ocean Grill and past it before heading back to the restaurant. Then we took the boat back afterwards. We were at the 3 PM lunch seating. Nice grilled vegetable plate, really good smoked marlin tostadas, and very nice fish of the day with the special sauce (made w/ coconut). Grilled octopus was very tender. Special margarita of the day was made with mint and was delightful, but later when we ordered a piña colada, it wasn't good at all. I think they used only fresh pineapple, which wasn't particularly sweet, so the whole drink tasted unbalanced. I actually found this to be the case w/ all piña coladas I tried in Puerto Vallarta, so maybe it's just better to stick to margaritas. The great dane was very cute and drooled a lot.
Coco's Kitchen - We stayed very close to here and went for brunch on Christmas. Service was very slow and the huevos rancheros were pretty plain and boring. However, the churro French toast was fantastic, the coffee was good, and the ambiance is delightful. I'd probably go back, but would perhaps stick with non-Mexican items or sweet breakfasts.
La Palapa - Ate here on our last night, after we couldn't get in to another place that we wanted to try. Service here was mediocre, drinks were super sweet and not good. The menu was interesting — sort of just generically tropical themed. I didn't like much about this place except the food, which was actually quite good. Coconut shrimp were just like how you'd want them to be. Catch of the day had an interesting array of sauces and sides, and the shrimp dish I ordered did too. So, all in all, I'd say the food menu is fun and tropical and they execute it well, while everything else just felt touristy and crowded.
El Arrayan - This place almost belongs in the "Very Good" category because I think it was better than La Palapa and Coco's. We were here on Christmas Eve, the night we arrived, and we had a reservation which was good, since it was crowded. The empanadas de platano appetizer was fantastic, and I also liked the three dipping sauces they give you. None of the salsas were spicy though, and it seemed like perhaps the only hot salsa they had was bottled? This seemed hard to believe, but when we asked for spicy salsa, bottles were all we got. Drinks here were good. Coconut colada and mango daiquiri were both well made. We had the chile en nogada here, which was quite good, but not as good as Red Cabbage. We also had the duck carnitas, which was disappointing. The duck was chopped up into small cubes and didn't contain much fat or pieces that pulled apart easily. It was nothing like carnitas. The duck carnitas in Oakland, CA at Cosecha is way better. Service here was good and friendly, and there were a lot of families eating there.
Taco Stands - We used this map which was very helpful: http://vallartainfo.com/street-food/ Unfortunately, the places we tried weren't that amazing (although they weren't bad). Mendoza's taco truck (at corner of Insurgentes and Cardenas) was mediocre, and we should have just ordered from the next one over, which was La Horniga. We only had one thing from there, and it was much better.
The Famous Churro Man -- See map linked above. I was excited to find this place, and actually go when they were open (between 4 pm and 8 pm), but once there, I didn't think the churros were that amazing. They were freshly fried, but were quite thin, so they were fairly crispy. I prefer a thicker style that's a little more chewy. One churro costs 1 peso so it's definitely a good deal. Man who was making churros was super nice.
Green Chairs -- We spent a day at this place on the beach in Zona Romantica, which is technically called something else, and is just south of Blue Chairs. Good drinks, both alcoholic and non-alcoholic smoothies. Chicken fingers were tasty. Good shrimp cocktail.
Overall, it was a great trip, and we're excited to return someday and enjoy more beach time and good food.