I have been living in the central valley for the last two years. The best beaches for us have been those with low-key waves, especially since our little boy will just go head first into the waves and some beaches are down right dangerous.
The Nicoya Penninsula is pretty built up, especially around Tamarindo area, but Samara still has one end of the beach that is pretty village still. It's got a lovely palm terrace to hang a hammock from and splash in the waves and tidal pools on that end. The waves are fun but safe, with no strong rip tides and it is close to other beaches for adventures outside. The town is pretty small and even though there are hotels and restaurants on the beach at the other end, you can't actually SEE them. It's not like Jaco where the hotels are these big monstrosities blocking the sky. They are all below tree level and well hidden and set back. Plus you can ride your bike into town from the villagey end. We rented an apartment from the mother of a friend there and we paid 300 for two weeks for a two bedroom two bath about a ten minute walk from the beach...no pool or anything, but very nice...and even in the rainy season you will have most of the morning to be on the beach before the rain comes.
We also really love Herradura, but not everyone does. We love it because it's a camping beach and from Late Nov to the end of February families are camped all along the dirt road that lines the beach...so cute! The beach is a little pebbly and sometimes, because there is a marina in the bay, you can get a HUGE wave out of no where that can knock you on your bum, especially at high tide when the water gets deep FAST, but for the most part it is safe, and when the tide is out the beach is wide mud flat that is great for littleone's to splash in and it is LITTERED with Sand Dollars.
I also like Estrillos...Oeste has a little town...Este has no town, just houses and a handful of low-key family hotels along the beach...and Central is also just houses. You can rent a four bedroom house with a pool on the beach there for about 800 dollars (I have the card of a guy we used once I can send you his e-mail if you PM me)
Palo seco is also lovely, IMO.
The one thing about the southern pacific coast in the rainy season is that there are these little no-see-um bugs that STING like a MO-FO in the afternoon into the evening. It's not pleasant. The bites go away pretty quickly, but OWIE do they hurt. Apparently baby oil wards them off...but ummm...baby oil plus late afternoon sun on the equator...bad idea for my family.
I have heard great things about Dominical but I have not been there.
We have recently explored the southern tip of the Nicoya penninsula (I can give you more info next week when we have been there for a few days). We are going to Tambor which apart from a few huge beach resorts in the area seems really nice. a cute small town, with some really lovely homes in the area and close to a few bigger towns for ammenities. We are renting a "castle" (four bedrooms plus a guest house with it's own kitchen, a pool and huge tower that boasts a view of the whole coastline, from Montezuma to Jaco!) and we are paying 1800 for ten days (we're sharing with my SIL and her family and MIL) but I know the guy managing the property has smaller places in the area and that there is a discount for long term rentals.
I LOVED the beach there, it was safe and pretty (like picture postcard perfect) and not at all built up, plus it is close to a gazillion adventure things to do, three national parks, island tours, snorkeling, swimming, surfing...I am excited. I'll let you know what we see if you PM me.
My advice would be to rent a 4X4. In the rainy season roads can get washed out FAST and you often find yourself driving through rivers. More than once we have had to spend the night away from "home" because the roads were impassable in our wimpy little toyota carolla.
The carribean coast is nice, too, but that is hurricane season for them...soooo, you are definitely better off on the pacific side. You can always do a trip to Cahuita if you want to check it our for a few days....gorgeous park!