I've read on another board by a Tamarindo area business owner that the unusually high fecal and E-coli counts were a) due to where the tests were taken (according to him right next to the city's sewage drainage outlets), b) due to the unusually heavy rains that were washing out through the system back during the summer when the tests were taken and c) that steps have since been taken by the local authorities to deal with the matter (a small number of business shutdowns after, IMHO, an initial period of gov't denial that a problem really even existed). Whether this is just spin or rationalization by a guy who has a definite self-interest in Tamarindo's reputation or not is open to question. But, personally, I'd be very hesitant to go in the water there until newer and safer readings are taken and the problem is significantly improved.
Normally, I hate questions that include superlatives like the nicest or the best. Nicest to whom? Best for what? Fortunately, in this case the poster did specify his criteria but I'd still like some clarification.
Exactly what type of nightlife are you looking for? If P4P is what you have in mind, then Jaco is the obvious 1st choice for beach areas that also have that. Tamarindo would be a distant 2nd. And, from what I've read about the overpriced mongering opportunities in Quepos, I don't even bother with it there.
You mentioned swimming. Exactly how much swimming are you really going to want to do? Or do you really have more lying on the beach or other water activities in mind? A lot of CR beaches, including at Manuel Antonio, have pretty serious riptides so you have to be very careful about where you decide to go swimming for more than just water quality concerns. A few of the posters mentioned surfing conditions and there are a lot of great beaches in CR for that, but keep in mind that strong waves may be great for surfing but it is definitely not the greatest for swimming if that is really what you want to do. BTW, El V, if you get knocked around on a surfboard, as you inevitably will, you inevitably wind up swallowing far more ocean water then you'd ever would just swimming around.
Picturesque, crystal clear ocean to indulge in and soak in some nature? The surrounding nature doesn't get much better than it is at MA where the mountains and jungle come right up to the beach. The dividing line between the tropical rainforest and tropical dry forest ecosystems on CR's Pacific coast is north of there, roughly just above Jaco. As El V mentioned, along the farther northern coast it can be very dry and dusty at this time of year. That doesn't mean they still won't be nice, but it does mean they lose their biggest advantage over other CR beaches, which is that they're considerably greener during the summer rainy season than they are during the winter, without suffering from all the rain and humidity that afflicts the rest of CR at that time of year.
Another problem that I have with your criteria is that very often they're contradictory. The places with the most nightlife also tend to be the places with the most rampant over-development and that can work at cross-purposes with the tranquil unspoiled beauty that you also seem to seek. It doesn't mean those places can't also be beautiful. MA is as overdeveloped as any of these places, but fortunately they're largely been able to keep that from impacting the park too badly. That is why they limit MA park to 500 or fewer visitors at any one time. In general, however, IMHO the MOST beautiful places are also the places that DON'T have that type of (over)development.
If you want mongering opportunities as your nightlife, then Jaco is your best bet. The beach in town really sucks, but you can take a cab to nearby beaches that are much nicer. It is also the easiest to get to from SJ (2.5 hrs by bus). Tamarindo would be your (distant) 2nd choice for mongering but then there is that question about the water (btw, the water right in front of Jaco is probably no great shakes either). It like all of the Guanacaste beaches are also a much longer drive (5.5 hrs by bus).
For more regular type nightlife, places like Tamarindo and MA rise in the ranking because they haven't become quite the social sewer that Jaco has and they offer somewhat greater natural beauty. Of just those 2, my personal pick would be MA because it is so much closer and easier to get to than SJ (3.75 hrs by bus) and offers a simply gorgeous park with white sand beaches (btw volcanic black sand beaches sound wonderfully tropical and exotic and they're also somewhat cooler on your feet, but they can be very dirty to lounge upon)(the sand is more like mud than sugar). The negative there is that with a few exceptions the beaches there are better for lying on than swimming (not sure how the swimming is at Tamarindo, but it is known more as a surfing beach).
Personally, none of those 3 beach areas would be my pick, but nightlife is not nearly as important as natural beauty to me. Chesscat gave an interesting breakdown for a beach-hopping approach to Guanacaste that might enable you to enjoy the best of what each of those beaches have to offer (if you have transportation). I'm not sure how much your schedule allows for that, as it takes the better part of a day going each way to and from there (unless you fly). Plus there is the question of whether this is the best season for going up there vs. some other CR beach region.
The beach at Puerto Viejo may not be so good but the nearby beaches of Playa Uva and Manzanillo are among the nicest in CR. And the area does not have anywhere near the rampant overdevelopment that plagues the northern Guanacaste area. The lodgings tend to be a little more rustics and the restaurants and nightlife have a very agreeable though much more laidback caribbean feel to them (jah mahn). Oh yeah, and in terms of distance, it is about 4.5 hrs from SJ.
However I'll throw out 2 other beach areas that no one has mentioned yet that I would take over any of these. Dominical is about 2 hours south of MA (by bus probably just an hour by car) and a long 7 hours from SJ if you go direct, but you could also stop a long the way to break up the trip and see another aspect of CR at a cloudforest lodge along the Cerro de la Muerte and then return by way of MA (with a stopover for contrast) and that would make for a very nice CR loop. Dominical is a nice little fishing and surfing village that is just now starting to develop (like Quepos was 10 years ago). It doesn't have the nightlife of its larger cousins but it does have some.
The other beach areas that I'd suggest is at the tip of the Nicoya Peninsula (Sta Teresa, Mal Pais and Montezuma). You have to take the ferry across the bay from Puntarenas to get there, but it still takes less time then driving from SJ to Tamarindo. The reason it hasn't gotten quite the same rate of development as the Guanacaste beaches is because of its perceived remoteness and the fact that tiny Tambor airport hasn't been changed into an international airport like Liberia which now enables people to fly into CR directly through there and be at the Guanacaste beaches in not much more than an hour. Playa Tambor is known for having a disgusting non-ecofriendly megaresort, but the smaller towns to the south of that are known more for their funky surfer atmosphere, smaller hotels, beautiful beaches and even more beautiful sunsets.
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