We visited both of those places in July. Manuel Antonio NP does get crowded because it is small, but there is a reservation system in place to limit the number of visitors. I recommend booking the early morning tour through the NP to beat both the crowds and heat. The animals are high in the trees, so people will not be blocking your ability to see and take pictures of the animals. The perk of a tour is that your guide will have a scope through which to see the animals close up. Definitely find time to enjoy the beach in the NP, too. One of my favorite moments on the trip was swimming there. In terms of Arenal, the only place that comes to mind that gets crowded is the Mistico Hanging Bridges. Again, if you go early in the morning when it opens, you will be able to beat the crowds. I've been to Costa Rica three times and I haven't been bothered by the number of visitors as I do in some places in Europe. Just be aware that a lot of places require online reservations and limit number of visitors, so book in advance once you know what you want to do.